Personalized Site-Specific Immunomodulation

ABSTRACT

The invention provides methods of treating inflammation in a specific organ or tissue of an individual. The method involves determining whether the individual has previously been infected with at least one pathogen that is pathogenic in the specific organ or tissue; and administering to the individual an anti-inflammatory composition comprising antigenic determinants, the antigenic determinants selected or formulated so that together they are specific for the at least one pathogen. The pathogen may be an endogenous or exogenous pathogen, and may further be a bacterial pathogen, a viral pathogen, a fungal pathogen, a protozoan pathogen, or a helminth pathogen.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a Continuation application of U.S. application Ser.No. 14/632,726 filed Feb. 26, 2015, which application is a Continuationapplication of U.S. application Ser. No. 13/560,892 filed Jul. 27, 2012,now issued as U.S. Pat. No. 8,980,276, which application is aContinuation-in-Part application of U.S. application Ser. No. 13/359,441filed Jan. 26, 2012; which application is a Continuation-in-Partapplication of PCT Application Serial No. PCT/CA2011/000851 filed Jul.26, 2011; which application is: (I) a Continuation-in-Part applicationof U.S. application Ser. No. 13/019,208 filed Feb. 1, 2011, now issuedas U.S. Pat. No. 9,107,864; which application is a Continuation-in-Partapplication of U.S. application Ser. No. 12/843,296 filed on Jul. 26,2010, now issued as U.S. Pat. No. 8,501,198; and (II) pursuant to 35U.S.C. § 119 (e), claims priority to the filing date of U.S. ProvisionalPatent Application Ser. No. 61/411,371 filed Nov. 8, 2010 and U.S.Provisional Patent Application Ser. No. 61/500,836 filed Jun. 24, 2011.The disclosures of all of the applications listed in this paragraph areherein incorporated by reference.

FIELD OF THE INVENTION

In various aspects, the invention relates to immunological therapies fortreating a condition characterized by inflammation. In alternativeembodiments, the invention provides methods of personalizingimmunomodulation therapy based on an individual's prior exposure to apathogen.

BACKGROUND OF THE INVENTION

More than one in three people in the developed nations are diagnosedwith cancer. More than one in four die from it. Therapies for cancerhave primarily relied upon treatments such as surgery, chemotherapy, andradiation. These approaches however, while beneficial for some types andstages of cancer, have proved to be of limited efficacy in many commontypes and stages of cancers. For example, surgical treatment of a tumorrequires complete removal of cancerous tissue to prevent reoccurrence.Similarly, radiation therapy requires complete destruction of cancerouscells. This is difficult since, in theory, a single malignant cell canproliferate sufficiently to cause reoccurrence of the cancer. Also, bothsurgical treatment and radiation therapy are directed to localized areasof cancer, and are relatively ineffective when the cancer metastasizes.Often surgery or radiation or both are used in combination with systemicapproaches such as chemotherapy. Chemotherapy however has the problem ofnon-selectivity with the concomitant problem of deleterious sideeffects, as well as the possibility of the cancer cells developingresistance to the drugs.

The inherent shortcomings of chemotherapy have led to disparate effortsto recruit various aspects of the immune system to treat cancers. Asubset of this work relates to immunization with microbial vaccines.Although this approach has a relatively long history, as discussed inmore detail below, the field is a very confused mixture of sometimesintriguing successes mixed with many failures that together have failedto produce a cohesive therapeutic approach amenable to widespreadclinical adoption.

Alternative approaches for the treatment of cancers have includedtherapies that involve augmentation of immune system function such ascytokine therapy (for e.g., recombinant interleukin 2 and gammainterferon for kidney cancers), dendritic cell therapy, autologous tumorvaccine therapy, genetically-altered vaccine therapy, lymphocytetherapy, and microbial vaccine therapies, the latter being thought toengage the host system in a non-specific manner. Microbial vaccines havebeen used to vaccinate subjects against pathogens that are associatedwith cancer, such as the human papillomavirus. Immunostimulatorymicrobial vaccines that are not targeted to cancer-causing organisms,i.e., non-specific immunostimulatory vaccines, such as pyrogenicvaccines, have a long clinical history that includes reports ofsuccesses and failures in treating a variety of cancers. For example,Coley's vaccine (a combination of Streptococcus pyogenes and Serratiamarcescens) has been reported to be helpful for the treatment ofsarcomas, and lymphomas (see, for e.g., Nauts H C, Fowler G A A, BogatoF H. A review of the influence of bacterial infection and of bacterialproducts [Coley's toxins] on malignant tumors in man. Acta Med Scand1953; 145 [Suppl. 276]:5-103). Clinical trials have reportedlydemonstrated the benefit of Coley's vaccine treatment for lymphoma andmelanoma (see, for e.g., Kempin S, Cirrincone C, Myers J et al: Combinedmodality therapy of advanced nodular lymphomas: the role of nonspecificimmunotherapy [MBV] as an important determinant of response andsurvival. Proc Am Soc Clin Oncol 1983; 24:56; Kolmel K F, Vehmeyer K.Treatment of advanced malignant melanoma by a pyrogenic bacteriallysate: a pilot study. Onkologie 1991; 14:411-17).

It has been suggested that the effectiveness of some non-specificbacterial cancer vaccines is attributable to particular bacterialcomponents or products, such as bacterial DNA or endotoxin (LPS), orbecause they induce the expression of particular factors, such as tumornecrosis factor (TNF) or interleukin-12. A correspondingly broad rangeof physiological mechanisms have been ascribed to such treatments,ranging from generalized effects of fever to anti-angiogenic mechanisms.In accordance with these various principles, a wide variety of microbialvaccines have been tested as general immune stimulants for the treatmentof cancer. While most have shown negative results, a few have shown someintriguing positive results in certain contexts, as discussed below.

Intradermal BCG (Mycobacterium bovis) vaccine treatment has beenreported to be effective for the treatment of stomach cancer (see, fore.g., Ochiai T, Sato J, Hayashi R, et al: Postoperative adjuvantimmunotherapy of gastric cancer with BCG-cell wall endoskeleton. Three-to six-year follow-up of a randomized clinical trial. Cancer ImmunolImmunother 1983; 14:167-171) and colon cancer (Smith R E, Colangelo L,Wieand H S, Begovic M, Wolmark N. Randomized trial of adjuvant therapyin colon carcinoma: 10-Year results of NSABP protocol C-01. J. NCI 2004;96[15]:1128-32; Uyl-de Groot C A, Vermorken J B, Hanna M G, Verboon P,Groot M T, Bonsel G J, Meijer C J, Pinedo H M. Immunotherapy withautologous tumor cell-BCG vaccine in patients with colon cancer: aprospective study of medical and economic benefits Vaccine 2005;23[17-18]:2379-87).

Mycobacterium w vaccine therapy, in combination with chemotherapy andradiation, was found to significantly improve quality of life andresponse to treatment in patients with lung cancer (see for e.g., Sur P,Dastidar A. Role of Mycobacterium w as adjuvant treatment of lung cancer[non-small cell lung cancer]. J Indian Med Assoc 2003 February;101[2]:118-120). Similarly, Mycobacterium vaccae vaccine therapy wasfound to improve quality of life (see, for e.g., O'Brien M, Anderson H,Kaukel E, et al. SRL172 [killed Mycobacterium vaccae] in addition tostandard chemotherapy improves quality of life without affectingsurvival, in patients with advanced non-small-cell lung cancer: phaseIII results. Ann Oncol 2004 June; 15[6]; 906-14) and symptom control(Harper-Wynne C, Sumpter K, Ryan C, et al. Addition of SRL 172 tostandard chemotherapy in small cell lung cancer [SCLC] improves symptomcontrol. Lung Cancer 2005 February; 47[2]:289-90) in lung cancerpatients.

Corynebacterium parvum vaccine was linked with a trend towards improvedsurvival for the treatment of melanoma (see, for e.g., Balch C M,Smalley R V, Bartolucci A A, et al. A randomized prospective trial ofadjuvant C. parvum immunotherapy in 260 patients with clinicallylocalized melanoma [stage I]. Cancer 1982 Mar. 15; 49[6]:1079-84).

Intradermal Streptococcus pyogenes vaccine therapy was found to beeffective for the treatment of stomach cancer (see, for e.g., Hanaue H,Kim D Y, Machimura T, et al. Hemolytic streptococcus preparation OK-432;beneficial adjuvant therapy in recurrent gastric carcinoma. Tokai J ExpClin Med 1987 November; 12[4]:209-14).

Nocardia rubra vaccine was found to be effective for the treatment oflung cancer (see, for e.g., Yasumoto K, Yamamura Y. Randomized clinicaltrial of non-specific immunotherapy with cell-wall skeleton of Nocardiarubra. Biomed Pharmacother 1984; 38[1]:48-54; Ogura T. Immunotherapy ofrespectable lung cancer using Nocardia rubra cell wall skeleton. Gan ToKagaku Ryoho 1983 February; 10[2 Pt 2]:366-72) and linked to a trend toimproved survival for the treatment acute myelogenous leukemia (Ohno R,Nakamura H, Kodera Y, et al. Randomized controlled study ofchemoimmunotherapy of acute myelogenous leukemia [AML] in adults withNocardia rubra cell-wall skeleton and irradiated allogeneic AML cells.Cancer 1986 Apr. 15; 57[8]:1483-8).

Lactobacillus casei vaccine treatment combined with radiation was foundto more effective for the treatment of cervical cancer than radiationalone. (see, for e.g., Okawa T, Kita M, Arai T, et al. Phase IIrandomized clinical trial of LC9018 concurrently used with radiation inthe treatment of carcinoma of the uterine cervix. Its effect on tumorreduction and histology. Cancer 1989 Nov. 1; 64[9]:1769-76)

Pseudomonas aeruginosa vaccine treatment was found to increase theeffectiveness of chemotherapy in the treatment of lymphoma and lungcancer (see, for e.g., Li Z, Hao D, Zhang H, Ren L, et al. A clinicalstudy on PA_MSHA vaccine used for adjuvant therapy of lymphoma and lungcancer. Hua Xi Yi Ke Da Xue Xue Bao 2000 September; 31 [3]:334-7).

Childhood vaccination with the smallpox vaccine (i.e., Vaccinia virusvaccine) was found to be associated with a decreased risk of melanomalater in life (see, for e.g., Pfahlberg A, Kolmel K F, Grange J M. etal. Inverse association between melanoma and previous vaccinationsagainst tuberculosis and smallpox: results of the FEBIM study. J InvestDermatol 2002[119]:570-575) as well as decreased mortality in thosepatients who did develop melanoma (see, for e.g., Kolmel K F, Grange JM, Krone B, et al. Prior immunization of patients with malignantmelanoma with vaccinia or BCG is associated with better survival.European Organization for Research and Treatment of Cancer cohort studyon 542 patients. Eur J Cancer 41 [2005]:118-125).

Treatment with rabies virus vaccine was found to result in temporaryremission in 8 of 30 patients with melanoma (see, for e.g., Higgins G,Pack G. Virus therapy in the treatment of tumors. Bull Hosp Joint Dis1951; 12:379-382; Pack G. Note on the experimental use of rabies vaccinefor melanomatosis. Arch Dermatol 1950; 62:694-695).

In spite of substantial efforts to engage the immune system to combatcancers using non-specific immunostimulatory microbial vaccines, thevast majority of these efforts have failed and there is little clinicalor research evidence of widespread success in improving the survival ofcancer patient populations. While it has been recognized thatimmunostimulatory microbial vaccine approaches have promise, it has alsobeen recognized that significant challenges characterize the field (see,for e.g., Ralf Kleef, Mary Ann Richardson, Nancy Russell, CristinaRamirez. “Endotoxin and Exotoxin Induced Tumor Regression with SpecialReference to Coley Toxins: A Survey of the Literature and PossibleImmunological Mechanisms.” Report to the National Cancer InstituteOffice of Alternative and Complementary Medicine August 1997; DL Mager.“Bacteria and Cancer: Cause, Coincidence or Cure? A Review.” Journal ofTranslational Medicine 28 Mar. 2006 4[14]:doi:10.1186/1479-5876-4-14).

In addition to treating cancers, immunomodulatory therapies have alsobeen used in the treatment of a wide variety of conditions characterizedby inflammation. For example, inflammatory bowel disease (IBD) is a namefrequently given to a group of inflammatory conditions of the colon andsmall intestine, generally characterized by similar symptoms andindeterminate etiology. Major sub-types of IBD are recognized clinicallyas Crohn's disease and ulcerative colitis. In addition to Crohn'sdisease and ulcerative colitis, IBD may also include conditionsrecognized as any one of the following: collagenous colitis, lymphocyticcolitis, ischaemic colitis, diversion colitis, Behçet's syndrome orindeterminate colitis. The difference between these conditions relateprimarily to the location and nature of the inflammatory changes in thegastrointestinal tract (GIT). Crohn's disease, for example, is generallyrecognized as potentially affecting any part of the gastrointestinaltract, from mouth to anus, with a majority of the cases marked byrelapsing and remitting granulomatous inflammation of the alimentarytract in the terminal ileum and colon. Ulcerative colitis, in contrast,is generally considered to be restricted to the colon and the rectum.The various regions of the gastrointestinal tract in which theseinflammatory conditions may exhibit symptoms include: the bowel orintestine, including: the small intestine (which has three parts: theduodenum, the jejunum, and the ileum); the large intestine (which hasthree parts: the cecum, the colon, which includes the ascending colon,transverse colon, descending colon and sigmoid flexure; and the rectum);and, the anus.

The understanding of inflammatory bowel diseases is evolving, but is asyet incomplete in many respects (see, for e.g., Baumgart D C, Carding SR (2007) “Inflammatory bowel disease: cause and immunobiology” TheLancet 369 (9573): 1627-40; Baumgart D C, Sandborn W J (2007)“Inflammatory bowel disease: clinical aspects and established andevolving therapies” The Lancet 369 (9573): 1641-57; Xavier R J, PodolskyD K (2007) “Unravelling the pathogenesis of inflammatory bowel disease”Nature 448 (7152): 427-34; J. H. Cho (2008) “The genetics andimmunopathogenesis of inflammatory bowel disease” Nature ReviewsImmunology 8, 458-466).

Anti-inflammatory drugs and immune system suppressants may be used inthe treatment of IBD, such as sulfasalazine (Azulfidine™), mesalamine(Asacol™, Rowasam), corticosteroids (e.g. prednisone), azathioprine(Imuran™), mercaptopurine (Purinethol), infliximab (Remicade™),adalimumab (Humira™), certolizumab pegol (Cimzia™), methotrexate(Rheumatrexm), cyclosporine (Gengraf™, Neoral™, Sandimmune™) ornatalizumab (Tysabri™).

Alternative treatments for IBD have been suggested, including the use ofvarious biological agents, or treatments that purportedly adjust naturalintestinal flora, sometimes called probiotic treatments (US2007/0258953; US 2008/0003207; WO 2007/076534; WO 2007/136719; WO2010/099824). It has for example been reported that IBD may be treatedwith a deliberate infestation of parasitic worms, for example byconsumption of the live ova of the Trichuris suis helminth (Summers etal. (2003) “Trichuris suis seems to be safe and possibly effective inthe treatment of inflammatory bowel disease”. Am. J. Gastroenterol. 98(9): 2034-41; Büning et al., (2008) “Helminths as governors ofinflammatory bowel disease” Gut 57:1182-1183; Weinstock and Elliott(2009) “Helminths and the IBD hygiene hypothesis” Inflamm Bowel Dis.2009 January; 15(1):128-33).

IBD is representative of a long list of conditions that arecharacterized by pathological inflammation, for which symptomatictreatment with anti-inflammatory medications is a common approach, oftenin the absence of a clear understanding of the etiology of the disease.Many of these inflammatory diseases, such as IBD and arthritis, are verycommon, but remain difficult to treat.

SUMMARY OF THE INVENTION

In one aspect, the invention provides methods and compositions fortreating an individual for a condition characterized by inflammation ordisease in a specific organ or tissue. The methods may involvedetermining whether the individual has previously been infected with atleast one pathogen that is pathogenic in the specific organ or tissue;and administering to the individual a therapeutic composition comprisingantigenic determinants, the antigenic determinants selected orformulated so that together they are specific for the at least onepathogen.

In another aspect, the invention provides methods of formulatingcompositions of the invention for treating an individual for a conditioncharacterized by disease or inflammation in a specific organ or tissue.The methods may involve determining whether the individual haspreviously been infected with at least one pathogen that is pathogenicin the specific organ or tissue; producing an antigenic compositioncomprising antigenic determinants that together are specific for the atleast one pathogen; and formulating the antigenic composition foradministration as a therapeutic or anti-inflammatory composition capableof eliciting an immunological or anti-inflammatory response in thespecific organ or tissue.

The methods detailed herein may involve identifying the presence of atleast one antibody that recognizes the at least one pathogen. Themethods may also or alternatively involve identifying at least onememory B cell that recognizes the at least one pathogen. The methods mayalso or alternatively involve identifying at least one memory T cellthat recognizes the at least one pathogen. The methods may for exampleinvolve obtaining the antibody, the memory B cell, or the memory T cellfrom peripheral circulation or from the targeted specific organ ortissue of the individual.

In another aspect, the invention provides methods of treating anindividual for a condition or disease or inflammation in a specificorgan or tissue. The method may involve administering to the individualan infectious dose of at least one pathogen that is pathogenic in thespecific organ or tissue, such as an attenuated pathogen; andadministering to the individual an anti-inflammatory compositioncomprising antigenic determinants, the antigenic determinants selectedor formulated so that together they are specific for the at least onepathogen, such as a composition comprising killed whole pathogens. Themethod may involve these two administration steps occurringsimultaneously. The method may involve the second step occurring between1 hour and 30 days after the first step.

Diseases or conditions that may be treated in accordance withalternative aspects of the invention includes cancers characterized bythe presence of a tumour in the specific organ or tissue of theindividual. Alternative diseases or conditions include autoimmunediseases characterized by an immune reaction in the specific organ ortissue that is targeted for treatment, such as arthritis or IBD.

Compositions of the invention may for example be formulated or used foradministration at a site that is distinct from the specific organ ortissue that is targeted for treatment, for example by subcutaneousinjection or intradermal injection. Compositions may for example beformulated for repeated administration, for example by subcutaneous orintradermal injection. In selected embodiments, compositions of theinvention may be formulated or used so as to produce a localized immuneresponse at a site of administration, for example at a site of injectionin the skin.

In selected embodiments, pathogens may be selected for use in methodsand compositions of the invention on the basis that the pathogen isendogenous to the specific organ or tissue that is targeted fortreatment. Alternatively, the pathogen may be exogenous to the specificorgan or tissue. The pathogen may be formulated as an attenuated or akilled pathogen, for example to provide anantigenic composition of wholeattenuated or killed pathogens. For example, the pathogen may be abacterium, a virus, a protozoa, a fungus, or a helminth.

In a further aspect, a method of formulating an anti-inflammatorycomposition for treating a condition characterized by inflammation in aspecific organ or tissue is provided. The method involves selecting atleast one pathogen that is pathogenic in the specific organ or tissue;producing an antigenic composition comprising antigenic determinantsthat together are specific for the pathogen; and formulating theantigenic composition for administration as an anti-inflammatorycomposition capable of eliciting an anti-inflammatory response in thespecific organ or tissue, for example wherein the conditioncharacterized by inflammation is not a cancer, for example wherein thecondition is IBD or arthritis.

The method may further involve a diagnostic step of identifying thespecific organ or tissue within which the inflammation is symptomaticprior to producing the antigenic composition. Optionally, a tumor orproliferative condition may be situated in the specific organ or tissue.

Optionally, the antigenic composition may be formulated for subcutaneousinjection or intradermal injection. Optionally, the antigeniccomposition may be formulated for injection to produce a localized skinimmune response at a site of administration. Optionally, the methoddetailed herein is provided such that when a specific tissue or organ isdetermined, the pathogen is selected from a particular group ofpathogens as described herein. In one aspect the pathogen is one that isan endogenous organism, which is a natural cause of infection in thetissue or organ in question. Optionally, the pathogen is an exogenousorganism that is a natural cause of infection in the tissue or organ isquestion, and may include, for example, a bacteria, virus, helminth, orfungus.

Optionally, the antigenic composition may be formulated for repeatedsubcutaneous or intradermal administration. Optionally, the antigeniccomposition may be formulated for administration by a route that is notenteric. Optionally, the pathogen detailed herein is a bacteria, avirus, a protozoa, a fungus or a helminth. Further, the method mayinvolve killing or attenuating the pathogen to formulate the antigeniccomposition as a whole killed or attenuated pathogen composition. Thepathogen may be a member of a species of the endogenous flora that is anatural cause of infection in the specific organ or tissue. The pathogenmay be an exogenous species that is a natural cause of infection in thespecific organ or tissue.

In another aspect, a method of treating an individual for a conditioncharacterized by inflammation in a specific organ or tissue is provided.The method involves administering to the individual an anti-inflammatorycomposition comprising antigenic determinants. The antigenicdeterminants are selected or formulated so that together they arespecific for at least one pathogen that is pathogenic in the specificorgan or tissue. Optionally, the anti-inflammatory composition may beadministered at an administration site in successive doses given at adosage interval of between one hour and one month, over a dosageduration of at least two weeks. Further, and without limitation, thedosing may comprise two or more doses over a period from four (4) daysto one (1) week.

In another aspect, use of an anti-inflammatory composition for treatingan individual for a condition characterized by inflammation in aspecific organ or tissue is disclosed. The anti-inflammatory compositioncontains antigenic determinants selected or formulated so that togetherthey are specific for at least one microbial pathogen that is pathogenicin the specific organ or tissue.

In another aspect, use of an anti-inflammatory composition to formulatea medicament for treating an individual for a condition characterized byinflammation in a specific organ or tissue is disclosed. Theanti-inflammatory composition contains antigenic determinants selectedor formulated so that together they are specific for at least onemicrobial pathogen that is pathogenic in the specific organ or tissue.

Optionally, the uses disclosed herein include those in which theindividual has a cancer situated in the organ or tissue. Further, andoptionally, the anti-inflammatory composition may be administered at anadministration site in successive doses given at a dosage interval ofbetween one hour and one month, over a duration of at least two weeks.Further, and without limitation, the dosing may comprise two or moredoses over a period from four (4) days to one (1) week.

In one aspect, a method of comparing immune responses is provided. Themethod involves administering to an animal having an organ or tissue amedicament having an antigenic composition having antigenic determinantsselected or formulated so that together the antigenic determinants arespecific for at least one microbial pathogen that is pathogenic in theorgan or tissue, extracting a quantifiable immune sample from the organor tissue, measuring a characteristic of the immune response in theorgan or tissue in the quantifiable immune sample following theadministration of the medicament, and, comparing the characteristic ofthe immune response in the quantifiable immune sample to a correspondingcharacteristic of the immune response in a reference immune sampleobtained from a corresponding organ or tissue. Optionally, the referenceimmune sample may be obtained from the corresponding organ or tissue inthe animal prior to the step of administering the medicament.Optionally, the reference immune sample may be obtained from thecorresponding organ or tissue in a second animal. Optionally, the animalmay have a cancer situated in the organ or tissue.

Comparing the characteristic of the immune response may involvecomparing, in the quantifiable and reference immune samples, anindication of the numbers of any one or more of the following cells:inflammatory monocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells,CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells.Optionally, the macrophages may include any one or more of thefollowing: M1-like macrophages or M2-like macrophages. Further,comparing the characteristic of the immune response may involvecomparing a shift in an activation state of macrophages. Optionally, themacrophages may shift from being M2-like macrophages to being M1-likemacrophages. Further and optionally, the macrophages may shift frombeing M1-like macrophages to being M2-like macrophages.

Optionally, comparing the characteristic of the immune response mayinvolve identifying, in the quantifiable and reference immune samples,cellular markers on any one or more of the following cells: inflammatorymonocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells, CD11c+ MHCclass II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Themacrophages may include any one or more of the following: M1-likemacrophages or M2-like macrophages.

Optionally, comparing the characteristic of the immune response mayinvolve identifying, in the quantifiable and reference immune samples,cytokines produced by any one or more of the following cells:inflammatory monocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells,CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Asdetailed herein, the macrophages may include any one or more of thefollowing: M1-like macrophages or M2-like macrophages. Optionally, thecytokines are produced as a result of a shift in an activation state ofthe macrophages. Optionally, the macrophages shift from being M2-likemacrophages to being M1-like macrophages. Further and optionally, themacrophages shift from being M1-like macrophages to being M2-likemacrophages.

Optionally, comparing the characteristic of the immune response mayinvolve identifying, in the quantifiable and reference immune samples,differential gene expression produced by any one or more of thefollowing cells: inflammatory monocytes, macrophages, CD1l b+Gr-1+cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ Tcells, or NK cells. The macrophages may include any one or more of thefollowing: M1-like macrophages or M2-like macrophages. Optionally, thedifferential gene expression is produced as a result of a shift in anactivation state of the macrophages. Optionally, macrophages may shiftfrom being M2-like macrophages to being M1-like macrophages. Further andoptionally, the macrophages shift from being M1-like macrophages tobeing M2-like macrophages.

Optionally, the medicament may be administered at an administration sitein successive doses given at a dosage interval of between one hour andone month, over a dosage duration of at least one week. Optionally, themedicament may be administered intradermally or subcutaneously.Optionally, the medicament may be administered in a dose so that eachdose is effective to cause a visible localized inflammatory immuneresponse at the administration site. Optionally, the medicament may beadministered so that visible localized inflammation at theadministration site occurs within 1 to 48 hours. Further and optionally,the animal may be a mammal. Optionally, the animal may be a human or amouse.

In another aspect, a method of selecting a therapeutic preparationsuitable for treating an individual for a cancer in a specific organ ortissue is provided. The method involves providing an animal having acancer situated in a specific organ or tissue, providing a testpreparation having one or more antigenic determinants of a microbialpathogen which is pathogenic in the corresponding specific organ ortissue in a healthy individual, measuring a characteristic of the immuneresponse in a reference immune sample obtained from the organ or tissueof the animal, administering the test preparation to the animal,measuring a characteristic of the immune response in a quantifiableimmune sample obtained from a corresponding organ or tissue of theanimal, comparing the characteristic of the immune response in the inthe reference and quantifiable immune samples, and treating an enhancedcharacteristic of the immune response in the quantifiable immune samplecompared to the reference immune sample as an indication of thesuitability of the test preparation as a therapeutic preparation.Optionally, the animal is sacrificed before the quantifiable immunesample has been obtained.

Optionally, comparing the characteristic of the immune response mayinvolve comparing, in the quantifiable and reference immune samples, anindication of the numbers of any one or more of the following cells:inflammatory monocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells,CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells.Optionally, the macrophages may include any one or more of thefollowing: M1-like macrophages or M2-like macrophages. Optionally,comparing the characteristic of the immune response may involvecomparing a shift in an activation state of macrophages. Optionally, themacrophages may shift from being M2-like macrophages to being M1-likemacrophages. Further and optionally, the macrophages may shift frombeing M1-like macrophages to being M2-like macrophages.

Optionally, comparing the characteristic of the immune response mayinvolve identifying, in the quantifiable and reference immune samples,cellular markers on any one or more of the following cells: inflammatorymonocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells, CD11c+ MHCclass II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Optionally,the macrophages may include any one or more of the following: M1-likemacrophages or M2-like macrophages.

Optionally, comparing the characteristic of the immune response mayinvolve identifying, in the quantifiable and reference immune samples,cytokines produced by any one or more of the following cells:inflammatory monocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells,CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Themacrophages may include any one or more of the following: M1-likemacrophages or M2-like macrophages. Optionally, the cytokines areproduced as a result of a shift in an activate state of the macrophages.Optionally, the macrophages may shift from being M2-like macrophages tobeing M1-like macrophages. Further, the macrophages may shift from beingM1-like macrophages to being M2-like macrophages.

Further and optionally, comparing the characteristic of the immuneresponse may involve identifying, in the quantifiable and referenceimmune samples, differential gene expression produced by any one or moreof the following cells: inflammatory monocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ Tcells, CD8+ T cells, or NK cells. Optionally, the macrophages mayinclude any one or more of the following: M1-like macrophages or M2-likemacrophages. Optionally, the differential gene expression may beproduced as a result of a shift in an activation state of themacrophages. Optionally, the macrophages may shift from being M2-likemacrophages to being M1-like macrophages. Further and optionally, themacrophages may shift from being M1-like macrophages to being M2-likemacrophages.

In another aspect, a method of selectively targeting an immune responseto a cancerous tissue or an organ in a human subject is provided. Themethod involves administering to the subject a medicament having aneffective amount of a microbial pathogen antigenic composition, whereinthe microbial pathogen may be pathogenic in the specific cancerous organor tissue of the subject and the antigenic composition comprisesantigenic determinants that together are specific for the microbialpathogen. Optionally, the antigenic composition may include a wholekilled bacterial cell composition. Optionally, the medicament may beadministered to the subject in an amount and for a time that iseffective to up-regulate an immune response in the cancerous organ ortissue of the subject. Optionally, the method may further involvemeasuring a characteristic of the immune response. The method alsoincludes treatment of pre-cancerous lesions including, but not limitedto, actinic keratosis, cervical dysplasia, and colonic adenomas.

In another aspect, a method for treating a human subject for a cancersituated in a tissue or an organ is provided. The method involvesadministering to the subject a medicament having an effective amount ofa microbial pathogen antigenic composition comprising a whole killedbacterial cell composition, wherein the microbial pathogen is pathogenicin the specific organ or tissue of the subject within which the canceris situated. The medicament may be administered to the subject in anamount and for a time that is effective to modulate an immune response.Optionally, the modulation of the immune response may involve a shift inthe activation state of macrophages. Optionally, the modulation of theimmune response may involve shifting from a M2-like macrophage responseto a M1-like macrophage response. The modulation of the immune responsemay involve a shift from M1-like macrophages to M2-like macrophages, asthose terms are defined herein. Optionally and without limitation, themethod may further involve measuring a characteristic of the immuneresponse.

Optionally, comparing the characteristic of the immune response mayinvolve comparing, in the quantifiable and reference immune samples, anindication of the numbers of any one or more of the following cells:inflammatory monocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells,CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells.Optionally, the macrophages may include any one or more of thefollowing: M1-like macrophages or M2-like macrophages. Optionally,comparing the characteristic of the immune response may involvecomparing a shift in an activation state of macrophages. Further andoptionally, the macrophages may shift from being M2-like macrophages tobeing M1-like macrophages. Optionally, the macrophages may shift frombeing M1-like macrophages to being M2-like macrophages.

Further and without limitation, comparing the characteristic of theimmune response may involve identifying, in the quantifiable andreference immune samples, cellular markers on any one or more of thefollowing cells: inflammatory monocytes, macrophages, CD11b+Gr-1+ cells,dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells,or NK cells. The macrophages may include any one or more of thefollowing: M1-like macrophages or M2-like macrophages. Optionally,comparing the characteristic of the immune response may involveidentifying, in the quantifiable and reference immune samples, cytokinesproduced by any one or more of the following cells: inflammatorymonocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells, CD11c+ MHCclass II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Optionally,the macrophages may include any one or more of the following: M1-likemacrophages or M2-like macrophages. Further, cytokines may be producedas a result of a shift in an activation state of the macrophages. Themacrophages may shift from being M2-like macrophages to being M1-likemacrophages. Optionally, the macrophages may shift from being M1-likemacrophages to being M2-like macrophages.

Further and optionally, comparing the characteristic of the immuneresponse may involve identifying, in the quantifiable and referenceimmune samples, differential gene expression produced by any one or moreof the following cells: inflammatory monocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ Tcells, CD8+ T cells, or NK cells. The macrophages may include any one ormore of the following: M1-like macrophages or M2-like macrophages.Optionally, the differential gene expression may be produced as a resultof a shift in an activation state of the macrophages. Further andoptionally, the macrophages may shift from being M2-like macrophages tobeing M1-like macrophages. The macrophages may shift from being M1-likemacrophages to being M2-like macrophages.

In another aspect, a method of monitoring efficacy of a treatment regimein an individual being treated for a cancer in a specific organ ortissue is provided. The method involves measuring a characteristic of animmune response in a post-treatment immune sample obtained from thespecific organ or tissue after the individual has been subject to thetreatment regime for a period of time, wherein the presence of acharacteristic of the immune response which is greater in magnitude thanwould be expected had the individual not been subject to the treatmentregime, is indicative of the efficacy of the treatment regime; and thetreatment regime involves administering a preparation comprising one ormore antigenic determinants of a microbial pathogen which is pathogenicin the corresponding specific organ or tissue in a healthy subject.

The method detailed herein may further involve measuring thecharacteristic of the immune response in a pre-treatment referencesample, wherein the pre-treatment reference sample was obtained from thespecific organ or tissue before, at the same time as or aftercommencement of the treatment regime, but prior to obtaining thepost-treatment immune sample, and comparing the characteristic of theimmune response in the pre-treatment and post-treatment samples, whereinan increase in the magnitude of the immune response in thepost-treatment immune sample compared to the pre-treatment referencesample is indicative of the efficacy of the treatment regime.Optionally, measuring the characteristic of the immune response mayinvolve determining an indication of the number of inflammatorymonocytes in a sample of the organ or tissue. Optionally, measuring thecharacteristic of the immune response may involve determining anindication of the number of macrophages in a sample of the organ ortissue. The macrophages may include any one or more of the following:M1-like macrophages or M2-like macrophages.

As detailed herein in another aspect, the invention also providesmethods for formulating an immunogenic composition for treating a cancersituated in a specific organ or tissue in a mammal, such as humanpatient. The method may include selecting at least one microbialpathogen that is naturally pathogenic in the organ or tissue of themammal within which the cancer is situated. An antigenic composition maybe produced that includes antigenic determinants that together arespecific for or characteristic of the microbial pathogen.

A diagnostic step may be used to identify the specific organ or tissuewithin which the cancer is situated, prior to producing the antigeniccomposition targeted to the site of the cancer. The site of the cancermay be a primary site, or a secondary site of metastasis. The antigeniccomposition may be sufficiently specific that it would be capable ofeliciting an immune response in the mammal specific to the microbialpathogen. The antigenic composition may be a bacterial composition, forexample derived from a bacterial species or species that are endogenousto the flora of the patient or from an exogenous species or species. Inalternative embodiments, the antigenic composition may be derived from avirus or viruses. Accordingly, the microbial pathogen from which theantigenic composition is derived may be a virus. The microbial pathogenmay be killed. In alternative embodiments, the microbial pathogen may belive or attenuated. Immunogenic compositions of the invention may alsobe formulated or administered with anti-inflammatory modalities, such asan NSAID. The site of administration may be at a site distant from thesite of the cancer, for example in an organ or tissue that is not theorgan or tissue within which the cancer is situated, for example theskin or subcutaneous tissue.

The antigenic composition may for example be formulated for subcutaneousinjection, intradermal injection or oral administration. In embodimentsfor subcutaneous or intradermal injection, the dosing or formulation ofthe antigenic composition may be adjusted in order to produce alocalized immune reaction visible in the skin at the site ofadministration, for example an area of inflammation from 2 mm to 100 mmin diameter appearing, for example, 2-48 hours after administration andlasting, for example, 2-72 hours or longer. The antigenic compositionmay be formulated for repeated subcutaneous or intradermaladministration, for example at alternating successive sites.

In some embodiments, the invention involves methods of treating a mammalfor a cancer situated in a tissue or an organ. In alternativeembodiments, the treatment may anticipate the development of the cancerin the tissue, for example if the site of a primary tumour suggests thelikelihood of metastasis to a particular tissue or organ, then thepatient may be prophylactically treated to prevent or amelioratemetastasis to that tissue or organ. The method may include administeringto the subject an effective amount of an antigenic compositioncomprising antigenic determinants that together are specific for atleast one microbial pathogen. An aspect of the invention involves theuse of a microbial pathogen that is pathogenic in the specific organ ortissue of the mammal within which the cancer is situated. The antigeniccomposition may be administered, for example by subcutaneous orintradermal injection at an administration site, in successive dosesgiven at a dosage interval, for example of between one hour and onemonth, over a dosage duration, for example of at least 1 week, 2 weeks,2 months, 6 months, 1, 2, 3, 4, or 5 years or longer. Each injectiondose may for example be metered so that it is effective to cause visiblelocalized inflammation at the administration site, appearing, forexample, 1-48 hours after injection.

In another aspect, methods are provided for treating cancers of aspecific organ or tissue in a subject by administering one or moreantigens of one or more microbial pathogens, such as bacterial, viral orfungal species that are pathogenic in the specific organ or tissue.

In alternative embodiments, the pathogenic microbial species may becapable of causing infection naturally, (i.e., without humanintervention) in the specific organ or tissue in a healthy subject, ormay have caused an infection in the specific organ or tissue in ahealthy subject. In alternative embodiments, the antigen may beadministered by administering preparations derived from whole cells of amicrobial species. In alternative embodiments, the method may, forexample, include administering at least two or more microbial species,or administering at least three or more microbial species, and themicrobes may be bacteria or viruses. In alternative embodiments, themethod may further include administering a supplement or an adjuvant. Anaspect of the invention involves administering antigenic compositions soas to elicit an immune response in said subject.

In alternative embodiments, the microbial pathogen in the antigeniccomposition may be killed, and thus rendered non-infectious. In someembodiments, the antigenic composition is administered at a site distantfrom the cancer site, and in selected embodiments of this kind, methodsof the invention may be carried out so that they do not produceinfection at the cancer site.

As detailed herein, various aspects of the invention involve treatingcancers. In this context, treatment may be carried out so as to providea variety of outcomes. For example, treatment may: provoke an immunereaction that is effective to inhibit or ameliorate the growth orproliferation of a cancer; inhibit the growth or proliferation of cancercells or tumors; cause remission of a cancer; improve quality of life;reduce the risk of recurrence of a cancer; inhibit metastasis of acancer; or, improve patient survival rates in a patient population. Inthis context, extending the life expectancy of a patient, or patientpopulation, means to increase the number of patients who survive for agiven period of time following a particular diagnosis. In someembodiments, treatment may be of patients who have not responded toother treatments, such as patients for whom a chemotherapy or surgeryhas not been an effective treatment. Treatment in alternativeembodiments may for example be before or after onset of cancer. Forexample prophylactic treatment may be undertaken, for example ofpatients diagnosed as being at risk of a particular cancer. For examplea patient having a genetic or lifestyle predisposition to cancer of acertain tissue or organ may be treated with an immunogenic compositioncomprising antigenic determinants of a pathogen that is pathogenic inthat organ or tissue. Similarly, the prophylactic treatment ofmetastasis may be undertaken, so that patients having a primary cancerwith a propensity to metastasize to a particular tissue or organ may betreated with an immunogenic composition comprising antigenicdeterminants of a pathogen that is pathogenic in that organ or tissue.

In another aspect, a method of treating a cancer situated in a lung in asubject is provided. The method involves administering to the subject aneffective amount of an antigen of one or more microbial species that ispathogenic in the lung and administering to the subject an effectiveamount of a platinum-containing chemotherapeutic agent. The microbialspecies may be a viral pathogen or a bacterial pathogen or a fungalpathogen. Further, the microbial species may be an endogenous species oran exogenous species.

In another aspect, use of an effective amount of an antigen of one ormore microbial species that is pathogenic in the lung is provided toformulate a medicament for use with a platinum-containingchemotherapeutic agent for treating lung cancer in a subject. In anotheraspect, use of an effective amount of an antigen of one or moremicrobial species that is pathogenic in the lung is provided for usewith a platinum-containing chemotherapeutic agent for treating lungcancer in a subject. The microbial species may be a viral pathogen or abacterial pathogen or a fungal pathogen. Further, the microbial speciesmay be an endogenous species or an exogenous species.

In another aspect, a kit is provided. The kit includes an antigen of oneor more microbial species that is pathogenic in the lung, aplatinum-containing chemotherapeutic agent; and instructions forproviding the antigen and the platinum-containing chemotherapeutic agentto a subject in need thereof. The microbial species may be an endogenousbacterial pathogen. It may also be an exogenous pathogen and may, forexample, be a viral pathogen or an exogenous bacterial pathogen or afungal pathogen.

In various aspects, the invention provides methods for treatinginflammatory conditions or immune diseases. For example, the inventionprovides methods for formulating and using an immunogenic compositionfor treating an IBD or arthritis or another disease associated with aninflammatory condition. The IBD may for example be an IBD that issymptomatic in one or more regions of the GIT of a human patient, suchas Crohn's disease, ulcerative colitis, collagenous colitis, lymphocyticcolitis, ischaemic colitis, diversion colitis, Behçet's syndrome orindeterminate colitis. The treatment of the patient may involve adiagnostic step of identifying the region of the GIT within which theIBD is symptomatic. The formulation may comprise an antigeniccomposition comprising antigenic determinants that together are specificfor at least one pathogen, such as a bacteria, a virus, a protozoa or ahelminth, or a fungus that is pathogenic in the effected region of theGIT. The formulation may be prepared for administration as animmunogenic composition capable of eliciting an immune reaction to treatthe IBD. The composition may for example be formulated for a route thatis not enteric, such as subcutaneous injection or intradermal injection,for example to produce a localized skin immune response, such as aninflammatory response, at a site of administration. The pathogen fortreating immune diseases may be an endogenous organism, which is anatural cause of infection in the organ or tissue in question. Thepathogen may be an exogenous organism, which is a natural cause ofinfection in the tissue or organ in question, and may include, forexample, a bacteria, virus, helminth, or fungus.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a survival curve for a cumulative series of patientsdiagnosed with stage 3B or 4 inoperable lung cancer (all patients),comparing patients treated with MRV, patients not treated with the MRV,and a standard SEER survival curve.

FIG. 2 shows a survival curve for a cumulative series of patientsdiagnosed with stage 3B or 4 inoperable lung cancer (patients treatedfor at least 2 months with MRV), comparing patients treated with MRV,patients not treated with the MRV, and a standard SEER survival curve.

FIG. 3 shows a survival curve for a cumulative series of patientsdiagnosed with stage 3B or 4 lung cancer, illustrating the benefits oftreatment with the MRV composition of the invention, comparing patientstreated with MRV, patients not treated with the MRV, and a standard SEERsurvival curve.

FIG. 4 shows a survival curve for a cumulative series of patientsdiagnosed with stage 3B or 4 lung cancer, illustrating the effect oftreatments for at least 2 months, comparing patients treated with MRV,patients not treated with the MRV, and a standard SEER survival curve.

FIG. 5 shows a survival curve for a cumulative series of patientsdiagnosed with stage 3B or 4 lung cancer, illustrating the effect oftreatments for at least 6 months duration, comparing patients treatedwith MRV, patients not treated with the MRV, and a standard SEERsurvival curve.

FIG. 6 shows a survival curve for a cumulative series of 52 breastcancer patients with metastases to bone and/or lung, comparing patientstreated with MRV, patients not treated with the MRV, and a standard SEERsurvival curve.

FIG. 7 is a comparison of survival of a cumulative series of metastaticprostate cancer patients who had surgery or radiation to destroy theirprostate gland (and thus, the primary tumour) and who had detectablecancer limited to bone metastases, comparing patients treated with MRV,patients not treated with the MRV, and a standard SEER survival curve.

FIG. 8 shows a survival curve for a cumulative series of patientsinitially diagnosed with Stage 4 colorectal cancer, comparing patientstreated with PVF, patients treated with MRV, patients not treated withan antigenic composition and a standard SEER survival curve.

FIG. 9 shows a survival curve for a cumulative series of patientsinitially diagnosed with Stage 4 Colorectal Cancer, with date frompatients receiving treatment within 3 months of diagnosis, comparingpatients treated with PVF, patients treated with MRV, patients nottreated with an antigenic composition and a standard SEER survivalcurve.

FIG. 10 shows a survival curve for a cumulative series of stage 3B lungcancer patients who were treated with an oral antigen therapy, Respivax,compared to patients who did not use an antigenic composition.

FIG. 11 shows a survival curve for a cumulative series of patientsdiagnosed with stage 3B lung cancer, illustrating the benefits oftreatment with the MRV composition of the invention, comparing patientstreated with MRV, patients not treated with the MRV, and a standard SEERsurvival curve.

FIG. 12 shows a survival curve measured from date of first visit for acumulative series of patients diagnosed with stage 3B lung cancer,illustrating the benefits of treatment with the MRV composition of theinvention, comparing patients treated with MRV, patients not treatedwith the MRV, and a standard SEER survival curve.

FIG. 13 shows a survival curve for a cumulative series of patientsdiagnosed with stage 3B lung cancer whose first visit was within 3months of diagnosis, illustrating the benefits of early treatment withthe MRV composition of the invention, comparing patients treated withMRV and patients not treated with the MRV.

FIG. 14 shows a photograph of lungs from mice treated (row 1) andnot-treated (row 2) with K. pneumoniae cells-only vaccine followingchallenge with Lewis lung carcinoma cells, as described in Example 4Aherein. The bottom row (not-numbered) depicts lungs from mice that werenot exposed to the mouse model of lung cancer.

FIG. 15 shows the average tumor volume of mice treated [AB1-AB6] andnot-treated [AB-7] with bacterial vaccines following challenge with B16melanoma cells, as described in Example 4B herein.

FIG. 16 shows a survival curve of colon cancer model mouse groupstreated with or without a variety of bacterial vaccines, as described inExample 4C herein.

FIGS. 17A to 17C show shows the number of inflammatory monocytes anddendritic cells in the draining lymph node, lungs, and spleen followingtreatment with either a K. pneumoniae antigenic composition or PBS, asdescribed in Example 5A herein.

FIG. 18 shows the total number of monocytes and dendritic cells in thelung, peritoneum and spleen of mice following treatment with either a K.pneumoniae antigenic composition, an E. coli antigenic composition, orPBS, as described in Example 5B herein.

FIG. 19 shows the total number of CD4+ T cells, CD8+ T cells, and NKcells from mice treated with either a K. pneumoniae antigeniccomposition, an E. coli antigenic composition, or PBS, as described inExample 5B herein.

FIGS. 20A and 20B show the total number of (A) inflammatory monocytesand (B) CD4+ T cells, CD8+ T cells, and NK cells on either of day 9 or16 from mice treated with either heat-inactivated a K. pneumoniaeantigenic composition, a phenol-inactivated K. pneumoniae antigeniccomposition, or PBS, as described in Example 5C herein.

FIGS. 21A and 21B show the total number of (A) inflammatory monocytesand dendritic cells and (B) CD4+ T cells, CD8+ T cells, and NK cellsfrom mice treated with either a heat-inactivated K. pneumoniae antigeniccomposition, a phenol-inactivated K. pneumoniae antigenic composition,or PBS, as described in Example 5D herein.

FIG. 22 shows the total number of tumour nodules in mice treated witheither PBS, or different dosages of K. pneumoniae antigenic compositionas described herein.

FIG. 23 shows a photograph of lungs from mice treated with either PBS,or different dosages of K. pneumoniae antigenic composition as describedherein.

FIG. 24 shows the total number of tumour nodules in mice treated witheither PBS, or different dosages of K. pneumoniae antigenic compositionas described herein.

FIG. 25 shows the total number of tumour nodules in mice treated witheither PBS, or dosages of K. pneumoniae antigenic composition incombination (or not) with cisplatin as described herein.

FIG. 26 shows a survival curve for mice injected with Lewis Lungcarcinoma cells and treated with either (i) vehicle control; (ii)Cisplatin; (iii) antigenic composition or (iv) antigenic composition andCisplatin.

FIG. 27 shows the percentage of CD11 b+ myeloid cells in the blood onday 13 of the relevant experiment detailed herein.

FIG. 28 shows (left panel) the frequency of CD11 b+NK1.1− cells fromlungs of mice treated with various dosages of K. pneumoniae antigeniccompositions or with PBS control or (right panel) the frequency ofCD11b+NK1.1+ cells from lungs of mice treated with various dosages of K.pneumoniae antigenic compositions or with PBS control.

FIG. 29 shows the amounts of numerous cytokines detected (in pg/g) fromlung tissue derived from mice treated with various dosages of K.pneumoniae antigenic compositions or with PBS control.

FIG. 30 shows the amounts of numerous cytokines detected (in pg/ml) fromBAL fluid from mice treated with various dosages of K. pneumoniaeantigenic compositions or with PBS control.

FIG. 31 shows the relative gene expression ratios of NOS2 to Arg1 frommice treated with various dosages of K. pneumoniae antigeniccompositions or with PBS control.

FIG. 32 shows the relative frequency of CD206 expression in lungmacrophages from mice treated with various dosages of K. pneumoniaeantigenic compositions or with PBS control.

FIG. 33 shows the relative frequency of F4/80 expression in lungmacrophages from mice treated with various dosages of K. pneumoniaeantigenic compositions or with PBS control.

FIG. 34 shows the relative frequency of CD11 b+Gr-1+ cells detected fromthe colons of mice treated with either K. pneumoniae or E. coliantigenic compositions or with PBS control.

FIG. 35 shows the relative frequency of CD11 b Gr-1+ cells detected fromthe lungs of mice treated with either K. pneumoniae or E. coli antigeniccompositions or with PBS control.

FIG. 36 shows the relative frequency of CD11b+ cells that were M1-likeas isolated from subQ 4T1 tumours (left panel) and the relativefrequency of CD11 b+ cells that were M2-like as isolated from subQ 4T1tumours (right panel).

FIG. 37 shows the tumour volume (mm³) from mice treated with eitherindomethacin and PBS; or indomethacin and a S. aureus antigeniccomposition; or EtOH and PBS; or EtOH and a S. aureus antigeniccomposition [left panel]. The right panel of this Figure also shows therelative frequency and makeup of CD11 b+ cells in the tumours at day 11of the relevant experiment detailed herein.

FIG. 38 shows the relative frequency and makeup of CD11 b+ cells in thetumours at day 22 of the relevant experiment detailed herein.

FIG. 39 shows the tumour volume in cohorts of animals treated withIndomethacin, Indomethacin+ antigenic compositions, vehicle alone, orantigenic compositions alone.

FIG. 40 shows the percentage of CD11 b+ cells in the tumours of animalstreated with Indomethacin, Indomethacin+ antigenic compositions, vehiclealone, or antigenic compositions alone (Day 11 data).

FIG. 41 shows the percentage of CD11 b+ cells in the tumours of animalstreated with Indomethacin, Indomethacin+ antigenic compositions, vehiclealone, or antigenic compositions alone (Day 22 data).

FIG. 42 shows the percentage of CD11b+CD94+ cells in the tumours ofanimals treated with Indomethacin, Indomethacin+ antigenic compositions,vehicle alone, or antigenic compositions alone (Day 22 data).

FIGS. 43A and 43B show the relative expression of (A) Fizz1 and (B) Ym1in excised tumors as described herein.

FIGS. 44A to 44D show the relative expression of (A) Arg1 and (B) Fizz1from tumors and spleens [(C) and (D)] as described herein.

FIGS. 45A to 45D show the relative expression of Nos2 and Ym1 fromtumors and spleens as described herein.

FIG. 46 shows the amount of IFN-γ produced in the lungs of mice with andwithout tumours and with and without antigenic composition treatment asdescribed herein.

FIG. 47 shows the amount of IL-10 produced from bone marrow macrophagescultured overnight with K. pneumoniae antigenic composition, LPS, andmedia alone.

FIG. 48 shows the relative expression of IL-10 produced in the tumoursof mice under conditions described herein.

FIG. 49 shows a percentage of weight change in C57BL/6 mice treated withand without antigenic compositions derived from E. coli in a DSS-inducedcolitis mouse model.

FIG. 50 shows the levels of IL-17 present in colons from C57BL/6 micetreated with and without antigenic compositions derived from E. coli ina DSS-induced colitis mouse model.

FIG. 51 shows the clinical score of mice treated with and withoutantigenic compositions derived from E. coli in a DSS-induced colitismouse model.

FIG. 52 shows the weight change in mice treated with and withoutantigenic compositions derived from E. coli in a DSS-induced colitismouse model.

FIG. 53 shows the anti-tumour efficacy of antigenic compositions derivedfrom S. pneumoniae is determined by previous exposure to live S.pneumoniae. The top panel depicts the percent survival of mice treatedwith and without antigenic compositions derived from S. pneumoniae wherethere was no previous exposure to S. pneumoniae. The middle paneldepicts the percent survival of mice treated with and without antigeniccompositions derived from S. pneumoniae where there was either no priorexposure to S. pneumoniae or there was current colonization by S.pneumoniae. The bottom panel depicts the percent survival of micetreated with and without antigenic compositions derived from S.pneumoniae where there was either no prior exposure to S. pneumoniae orthere was past exposure to S. pneumoniae.

DETAILED DESCRIPTION OF THE INVENTION

In various aspects, the invention relates to the surprising discoverythat administration of formulations that include antigenic determinantsof microbial pathogens that are pathogenic in a particular tissue ororgan, is effective in treating inflammation or cancer situated in thatspecific tissue or organ. Compositions of the invention may for examplebe administed at a site that is distant from the site of inflammation orcancer. Accordingly, the invention provides antigenic compositionsderived from these microbial pathogens, including whole killedbacterial, viral or fungal species, or components thereof, for thetreatment of inflammation or cancer, and methods for using the same. Thecompositions may for example be derived from endogenous pathogens orexogenous pathogens, as described in more detail below.

Based on observations from treating patients, it was found thatadministering compositions of killed bacteria which included many of thebacterial species that commonly cause lung infection was surprisinglyand unexpectedly effective in improving the clinical course of cancer ofthe lung. Similarly, it was found that administering compositionsincluding killed Staphylococcus aureus, one of the most common causes ofbone, breast, skin, perineal and lymph node infection and septicemia wassurprising and unexpectedly effective in improving the clinical courseof cancer of the bone, breast, skin, perineum, and lymphoma (cancer ofthe lymph glands) and multiple myeloma (a type of hematological cancer).Similarly, it was surprisingly and unexpectedly found that administeringa composition including Escherichia coli, which is a common cause ofcolon, kidney, peritoneal, liver, abdominal, pancreatic and ovarianinfection, was effective in improving the clinical course of cancer inthe colon, kidney, peritoneum, liver, abdominal lymph nodes, pancreasand ovary.

These results indicate that a composition including antigens ofpathogenic microbial species that cause infection in a particular tissueor organ will be an effective formulation for treating a cancer in thattissue or organ. For example, cancer in the lung is effectively treatedwith a microbial composition including one or more pathogenic speciesthat commonly cause lung infection, while cancer in the colon iseffectively treated with a composition including pathogenic microbialspecies that commonly cause colon infections.

Antigenic compositions of the invention may be produced that includeantigenic determinants that together are specific for or characteristicof a microbial pathogen. In this context, by “specific”, it is meantthat the antigenic determinants are sufficiently characteristic of thepathogen that they could be used to raise an immune response, such as anadaptive immune response, against the pathogen in the patient, if theantigenic determinants were to be administered in an appropriate mannerto have that effect. It will be recognized that the antigenicdeterminants need not be so specific that they are characteristic ofonly one particular strain or species of pathogen, since even a specificimmune response against a particular pathogen may be cross reactive withother closely related organisms that are also naturally pathogenic inthe tissue or organ in which the cancer is situated and that theantigenic composition is formulated or selected to target.

In some embodiments, the compositions of pathogenic microbes may be usedfor treating primary cancer sites and/or sites of metastasis. Thus, forexample, the microbial compositions may be used for the treatment of acancer at a particular site, regardless of whether the cancer is aprimary cancer or a metastasis. The composition may be directed to thetreatment of each cancer site, or may be a combined composition for boththe primary cancer and the metastatic site(s). For example, to treatkidney cancer that has metastasized to the lung and bone, threedifferent compositions, including one or more species that are known tobe kidney pathogens, one or more species that are known to be lungpathogens and one or more species that are known to be bone pathogens,or a combined composition thereof may be used. In some embodiments, thecompositions may be administered in different locations at the same timeor at different times.

For example, for lung cancer with metastasis to the bone, in alternativeembodiments, both a microbial composition including one or morebacterial species (or viruses) which commonly cause lung infection and amicrobial composition including one or more bacterial species (orviruses) which commonly cause bone infection may be used. Similarly, forcolon cancer with metastasis to the lungs, both a pathogenic bacterial(or viral) composition including one or more bacterial species (orviruses) which commonly cause colon infection and a microbialcomposition including one or more bacterial species (or viruses) whichcommonly cause lung infection may be used; for prostate cancer withmetastasis to the bones, both a pathogenic bacterial (or viral)composition including one or more bacterial species (or viruses) whichcommonly cause prostate infection and a pathogenic bacterial (or viral)composition including one or more bacterial species (or viruses thatcommonly cause bone infection may be used. The pathogen for treatingimmune diseases may be an endogenous organism, which is a natural causeof infection in the organ or tissue in question. The pathogen may be anexogenous organism, which is a natural cause of infection in the tissueor organ in question, and may include, for example, a bacteria, virus,helminth, or fungus.

The following list provides some non-limiting examples of primarycancers and their common sites for secondary spread (metastases):

Primary cancer Common sites for metastases prostate bone, lungs breastbone, lungs, skin, liver, brain lung bone, brain, liver, lungs colonliver, lungs, bone, brain kidney lungs, bone, brain pancreas liver,lungs melanoma lungs, skin, liver, brain uterus lungs, bones, ovariesovary liver, lung bladder bone, lung, liver head and neck bone, lungssarcoma lungs, brain stomach liver cervix bone, lungs testes lungsthyroid bone, lungs

In some embodiments, the antigenic compositions may be used for treatingor preventing cancers at primary sites or for treating or preventingmetastasis. For example, in long-term smokers, an antigenic compositionspecific for cancer of the lung (for example including antigenicdeterminants of one or more bacterial species or viruses which commonlycause lung infection) may be used to appropriately stimulate the immunesystem to defend against the development of cancer within the lungtissue. As another example, an antigenic composition specific for cancerof the breast (for example including antigenic determinants of one ormore bacterial species which commonly cause breast infection) could beused to prevent breast cancer in women with a strong family history ofbreast cancer or a genetic predisposition. In alternative embodiments,an antigenic composition including one or more bacterial species whichcommonly cause bone infection may be used to prevent or treat bonemetastases in a patient with prostate cancer. In further alternativeembodiments, an antigenic composition including one or more bacterialspecies or viruses which commonly cause lung infection may be used toprevent or treat lung metastases in a patient with malignant melanoma.

Various alternative embodiments and examples of the invention aredescribed herein. These embodiments and examples are illustrative andshould not be construed as limiting the scope of the invention.

Cancers

Most cancers fall within three broad histological classifications:carcinomas, which are the predominant cancers and are cancers ofepithelial cells or cells covering the external or internal surfaces oforgans, glands, or other body structures (for e.g., skin, uterus, lung,breast, prostate, stomach, bowel), and which tend to metastasize;carcinomas, which are derived from connective or supportive tissue (fore.g., bone, cartilage, tendons, ligaments, fat, muscle); and hematologictumors, which are derived from bone marrow and lymphatic tissue.Carcinomas may be adenocarcinomas (which generally develop in organs orglands capable of secretion, such as breast, lung, colon, prostate orbladder) or may be squamous cell carcinomas (which originate in thesquamous epithelium and generally develop in most areas of the body).Sarcomas may be osteosarcomas or osteogenic sarcomas (bone),chondrosarcomas (cartilage), leiomyosarcomas (smooth muscle),rhabdomyosarcomas (skeletal muscle), mesothelial sarcomas ormesotheliomas (membranous lining of body cavities), fibrosarcomas(fibrous tissue), angiosarcomas or hemangioendotheliomas (bloodvessels), liposarcomas (adipose tissue), gliomas or astrocytomas(neurogenic connective tissue found in the brain), myxosarcomas(primitive embryonic connective tissue), or mesenchymous or mixedmesodermal tumors (mixed connective tissue types). Hematologic tumorsmay be myelomas, which originate in the plasma cells of bone marrow;leukemias which may be “liquid cancers” and are cancers of the bonemarrow and may be myelogenous or granulocytic leukemia (myeloid andgranulocytic white blood cells), lymphatic, lymphocytic, orlymphoblastic leukemias (lymphoid and lymphocytic blood cells) orpolycythemia vera or erythremia (various blood cell products, but withred cells predominating); or lymphomas, which may be solid tumors andwhich develop in the glands or nodes of the lymphatic system, and whichmay be Hodgkin or Non-Hodgkin lymphomas. In addition, mixed typecancers, such as adenosquamous carcinomas, mixed mesodermal tumors,carcinosarcomas, or teratocarcinomas also exist.

Cancers named based on primary site may be correlated with histologicalclassifications. For example, lung cancers are generally small cell lungcancers or non-small cell lung cancers, which may be squamous cellcarcinoma, adenocarcinoma, or large cell carcinoma; skin cancers aregenerally basal cell cancers, squamous cell cancers, or melanomas.Lymphomas may arise in the lymph nodes associated with the head, neckand chest, as well as in the abdominal lymph nodes or in the axillary oringuinal lymph nodes. Identification and classification of types andstages of cancers may be performed by using for example informationprovided by the Surveillance, Epidemiology, and End Results (SEER)Program of the National Cancer Institute, which is an authoritativesource of information on cancer incidence and survival in the UnitedStates and is recognized around the world. The SEER Program currentlycollects and publishes cancer incidence and survival data from 14population-based cancer registries and three supplemental registriescovering approximately 26 percent of the US population. The programroutinely collects data on patient demographics, primary tumor site,morphology, stage at diagnosis, first course of treatment, and follow-upfor vital status, and is the only comprehensive source ofpopulation-based information in the United States that includes stage ofcancer at the time of diagnosis and survival rates within each stage.Information on more than 3 million in situ and invasive cancer cases isincluded in the SEER database, and approximately 170,000 new cases areadded each year within the SEER coverage areas. The incidence andsurvival data of the SEER Program may be used to access standardsurvival for a particular cancer site and stage. For example, to ensurean optimal comparison group, specific criteria may be selected from thedatabase, including date of diagnosis and exact stage (for example, inthe case of the lung cancer example herein, the years were selected tomatch the time-frame of the retrospective review, and stage 3B and 4lung cancer were selected; and in the case of the colon cancer exampleherein, the years were also selected to match the time-frame of theretrospective review, and the stage 4 colon cancer was selected).

Cancers may also be named based on the organ in which they originatei.e., the “primary site,” for example, cancer of the breast, brain,lung, liver, skin, prostate, testicle, bladder, colon and rectum,cervix, uterus, etc. This naming persists even if the cancermetastasizes to another part of the body that is different from theprimary site. With the present invention, treatment is directed to thesite of the cancer, not type of cancer, so that a cancer of any typethat is situated in the lung, for example, would be treated on the basisof this localization in the lung.

A “cancer” or “neoplasm” is any unwanted growth of cells serving nophysiological function. In general, a cancer cell has been released fromits normal cell division control, i.e., a cell whose growth is notregulated by the ordinary biochemical and physical influences in thecellular environment. Thus, “cancer” is a general term for diseasescharacterized by abnormal uncontrolled cell growth. In most cases, acancer cell proliferates to form clonal cells that are malignant. Thelump or cell mass, “neoplasm” or “tumor,” is generally capable ofinvading and destroying surrounding normal tissues. By “malignancy”, asused herein, is meant as an abnormal growth of any cell type or tissuethat has a deleterious effect in the organism having the abnormalgrowth. The term “malignancy” or “cancer” includes cell growths that aretechnically benign but which carry the risk of becoming malignant.Cancer cells may spread from their original site to other parts of thebody through the lymphatic system or blood stream in a process known as“metastasis.” Many cancers are refractory to treatment and prove fatal.Examples of cancers or neoplasms include, without limitation,transformed and immortalized cells, tumors, carcinomas, in variousorgans and tissues as described herein or known to those of skill in theart.

A “cell” is the basic structural and functional unit of a livingorganism. In higher organisms, e.g., animals, cells having similarstructure and function generally aggregate into “issues” that performparticular functions. Thus, a tissue includes a collection of similarcells and surrounding intercellular substances, e.g., epithelial tissue,connective tissue, muscle, nerve. An “organ” is a fully differentiatedstructural and functional unit in a higher organism that may be composedof different types of tissues and is specialized for some particularfunction, e.g., kidney, heart, brain, liver, etc. Accordingly, by“specific organ, tissue, or cell” is meant herein to include anyparticular organ, and to include the cells and tissues found in thatorgan.

“Pathogenic” agents are agents, such as microbes, such as bacteria orviruses, which are known to cause infection in a host in nature, and inthis sense, “pathogenic” is used in the context of the present inventionto mean “naturally pathogenic”. Although a wide variety of microbes maybe capable of causing infection under artificial conditions, such asartificial inoculations of a microbe into a tissue, the range ofmicrobes that naturally cause infection is necessarily limited, and wellestablished by medical practice.

An “infection” is the state or condition in which the body or a part ofit is invaded by a pathogenic agent (e.g., a microbe, such as abacterium) which, under favorable conditions, multiplies and produceseffects that are injurious (Taber's Cyclopedic Medical Dictionary, 14thEd., C. L. Thomas, Ed., F. A. Davis Company, PA, USA). An infection maynot always be apparent clinically and may result in only localizedcellular injury. Infections may remain subclinical, and temporary if thebody's defensive mechanisms are effective. Infections may spread locallyto become clinically apparent as an acute, a subacute, or a chronicclinical infection or disease state. A local infection may also becomesystemic when the pathogenic agent gains access to the lymphatic orvascular system (On-Line Medical Dictionary,http://cancerweb.ncl.ac.uk/omd/). Infection is usually accompanied byinflammation, but inflammation may occur without infection.

“Inflammation” is the characteristic tissue reaction to injury (markedby swelling, redness, heat, and pain), and includes the successivechanges that occur in living tissue when it is injured. Infection andinflammation are different conditions, although one may arise from theother (Taber's Cyclopedic Medical Dictionary, supra). Accordingly,inflammation may occur without infection and infection may occur withoutinflammation (although inflammation typically results from infection bypathogenic bacteria or viruses). Inflammation is characterized by thefollowing symptoms: redness (rubor), heat (calor), swelling (tumor),pain (dolor). Localized visible inflammation on the skin may be apparentfrom a combination of these symptoms, particularly redness at a site ofadministration.

Various subjects may be treated in accordance with alternative aspectsof the invention. As used herein, a “subject” is an animal, for e.g, amammal, to whom the specific pathogenic bacteria, bacterial antigens,viruses, viral antigens or compositions thereof of the invention may beadministered. Accordingly, a subject may be a patient, e.g., a human,suffering from a cancer, or suspected of having a cancer, or at risk fordeveloping a cancer. A subject may also be an experimental animal, e.g.,an animal model of a cancer, as is described in Example 5. In someembodiments, the terms “subject” and “patient” may be usedinterchangeably, and may include a human, a non-human mammal, anon-human primate, a rat, mouse, dog, etc. A healthy subject may be ahuman who is not suffering from a cancer or suspected of having acancer, or who is not suffering from a chronic disorder or condition. A“healthy subject” may also be a subject who is not immunocompromised. Byimmunocompromised is meant any condition in which the immune systemfunctions in an abnormal or incomplete manner. Immunocompromisation maybe due to disease, certain medications, or conditions present at birth.Immunocompromised subjects may be found more frequently among infants,the elderly, and individuals undergoing extensive drug or radiationtherapy.

An “immune response” includes, but is not limited to, one or more of thefollowing responses in a mammal: induction or activation of antibodies,neutrophils, monocytes, macrophages (including both M1-like macrophagesand M2-like macrophages as described herein), B cells, T cells(including helper T cells, natural killer cells, cytotoxic T cells, γδ Tcells), such as induction or activation by the antigen(s) in acomposition or vaccine, following administration of the composition orvaccine. An immune response to a composition or vaccine thus generallyincludes the development in the host animal of a cellular and/orantibody-mediated response to the composition or vaccine of interest. Insome embodiments, the immune response is such that it will also resultin slowing or stopping the progression of a cancer in the animal. Animmune response includes both cellular immune responses and humoralimmune responses as understood by those persons skilled in the art.

Bacteria and Bacterial Colonizations and Infections

Most animals are colonized to some degree by other organisms, such asbacteria, which generally exist in symbiotic or commensal relationshipswith the host animal. Thus, many species of normally harmless bacteriaare found in healthy animals, and are usually localized to the surfaceof specific organs and tissues. Often, these bacteria aid in the normalfunctioning of the body. For example, in humans, symbiotic Escherichiacoli bacteria may be found in the intestine, where they promote immunityand reduce the risk of infection with more virulent pathogens.

Bacteria that are generally harmless, such as Escherichia coli, cancause infection in healthy subjects, with results ranging from mild tosevere infection to death. Whether or not a bacterium is pathogenic(i.e., causes infection) depends to some extent on factors such as theroute of entry and access to specific host cells, tissues, or organs;the intrinsic virulence of the bacterium; the amount of the bacteriapresent at the site of potential infection; or the health of the hostanimal. Thus, bacteria that are normally harmless can become pathogenicgiven favorable conditions for infection, and even the most virulentbacterium requires specific circumstances to cause infection.Accordingly, microbial species that are members of the normal flora canbe pathogens when they move beyond their normal ecological role in theendogenous flora. For example, endogenous species can cause infectionoutside of their ecological niche in regions of anatomical proximity,for example by contiguous spread. When this occurs, these normallyharmless endogenous bacteria are considered pathogenic.

Specific bacterial species and viruses are known to cause infections inspecific cells, tissues, or organs in otherwise healthy subjects.Examples of bacteria and viruses that commonly cause infections inspecific organs and tissues of the body are listed below; it will beunderstood that these examples are not intended to be limiting and thata skilled person would be able to readily recognize and identifyinfectious or pathogenic bacteria that cause infections, or commonlycause infections, in various organs and tissues in healthy adults (andrecognize the relative frequency of infection with each bacterialspecies) based on the knowledge in the field as represented, forexample, by the following publications: Manual of Clinical Microbiology8th Edition, Patrick Murray, Ed., 2003, ASM Press American Society forMicrobiology, Washington D.C., USA; Mandell, Douglas, and Bennett'sPrinciples and Practice of Infectious Diseases 5th Edition, G. L.Mandell, J. E. Bennett, R. Dolin, Eds., 2000, Churchill Livingstone,Philadelphia, Pa., USA, all of which are incorporated by referenceherein.

Infections of the skin are commonly caused by the following bacterialspecies: Staphylococcus aureus, Beta hemolytic streptococci group A, B,C or G, Corynebacterium diptheriae, Corynebacterium ulcerans, orPseudomonas aeruginosa; or viral pathogens: rubeola, rubella,varicella-zoster, echoviruses, coxsackieviruses, adenovirus, vaccinia,herpes simplex, or parvo B19.

Infections of the soft tissue (e.g., fat and muscle) are commonly causedby the following bacterial species: Streptococcus pyogenes,Staphylococcus aureus, Clostridium perfringens, or other Clostridiumspp.; or viral pathogens: influenza, or coxsackieviruses.

Infections of the breast are commonly caused by the following bacterialspecies: Staphylococcus aureus, or Streptococcus pyogenes.

Infections of the lymph nodes of the head and neck are commonly causedby the following bacterial species: Staphylococcus aureus, orStreptococcus pyogenes; or viral pathogens: Epstein-Barr,cytomegalovirus, adenovirus, measles, rubella, herpes simplex,coxsackieviruses, or varicella-zoster.

Infections of the lymph nodes of the arm/axillae are commonly caused bythe following bacterial species: Staphylococcus aureus, or Streptococcuspyogenes; or viral pathogens: measles, rubella, Epstein-Barr,cytomegalovirus, adenovirus, or varicella-zoster.

Infections of the lymph nodes of the mediastinum are commonly caused bythe following bacterial species: viridans streptococci, Peptococcusspp., Peptostreptococcus spp., Bacteroides spp., Fusobacterium spp., orMycobacterium tuberculosis, or viral pathogens: measles, rubella,Epstein-Barr, cytomegalovirus, varicella-zoster, or adenovirus.

Infections of the pulmonary hilar lymph nodes are commonly caused by thefollowing bacterial species: Streptococcus pneumoniae, Moraxellacatarrhalis, Mycoplasma pneumoniae, Klebsiella pneumoniae, Haemophilusinfluenza, Chlamydophila pneumoniae, Bordetella pertussis orMycobacterium tuberculosis; or viral pathogens: influenza, adenovirus,rhinovirus, coronavirus, parainfluenza, respiratory syncytial virus,human metapneumovirus, or coxsackievirus.

Infections of the intra-abdominal lymph nodes are commonly caused by thefollowing bacterial species: Yersinia enterocolitica, Yersiniapseudotuberculosis, Salmonella spp., Streptococcus pyogenes, Escherichiacoli, Staphylococcus aureus, or Mycobacterium tuberculosis; or viralpathogens: measles, rubella, Epstein-Barr, cytomegalovirus,varicella-zoster, adenovirus, influenza, or coxsackieviruses.

Infections of the lymph nodes of the leg/inguinal region are commonlycaused by the following bacterial species: Staphylococcus aureus, orStreptococcus pyogenes; or viral pathogens: measles, rubella,Epstein-Barr, cytomegalovirus, or herpes simplex.

Infections of the blood (i.e., septicemia) are commonly caused by thefollowing bacterial species: Staphylococcus aureus, Streptococcuspyogenes, coagulase-negative staphylococci, Enterococcus spp.,Escherichia coli, Klebsiella spp., Enterobacter spp., Proteus spp.,Pseudomonas aeruginosa, Bacteroides fragilis, Streptococcus pneumoniae,or group B streptococci; or viral pathogens: rubeola, rubella,varicella-zoster, echoviruses, coxsackieviruses, adenovirus,Epstein-Barr, herpes simplex, or cytomegalovirus.

Infections of the bone are commonly caused by the following bacterialspecies: Staphylococcus aureus, coagulase-negative staphylococci,Streptococcus pyogenes, Streptococcus pneumoniae, Streptococcusagalactiae, other streptococci spp., Escherichia coli, Pseudomonas spp.,Enterobacter spp., Proteus spp., or Serratia spp.; or viral pathogens:parvovirus B19, rubella, or hepatitis B.

Infections of the joint are commonly caused by the following bacterialspecies: Staphylococcus aureus, coagulase-negative staphylococci,Streptococcus pyogenes, Streptococcus pneumoniae, Streptococcusagalactiae, other streptococci spp., Escherichia coli, Pseudomonas spp.,Enterobacter spp., Proteus spp., Serratia spp., Neisseria gonorrhea,salmonella species, Mycobacterim tuberculosis, Hemophilus influenza; orviral pathogens: parvovirus B19, rubella, hepatitis B; or fungalpathogen: Scedosporium prolificans

Infections of the meninges are commonly caused by the followingbacterial species: Haemophilus influenzae, Neisseria meningitidis,Streptococcus pneumoniae, Streptococcus agalactiae, or Listeriamonocytogenes; or viral pathogens: echoviruses, coxsackieviruses, otherenteroviruses, or mumps.

Infections of the brain are commonly caused by the following bacterialspecies: Streptococcus spp. (including S. anginosus, S. constellatus, S.intermedius), Staphylococcus aureus, Bacteroides spp., Prevotella spp.,Proteus spp., Escherichia coli, Klebsiella spp., Pseudomonas spp.,Enterobacter spp., or Borrelia burgdorferi; or viral pathogens:coxsackieviruses, echoviruses, poliovirus, other enteroviruses, mumps,herpes simplex, varicella-zoster, flaviviruses, or bunyaviruses.

Infections of the spinal cord are commonly caused by the followingbacterial species: Haemophilus influenzae, Neisseria meningitidis,Streptococcus pneumoniae, Streptococcus agalactiae, Listeriamonocytogenes, or Borrelia burgdorferi; or viral pathogens:coxsackieviruses, echoviruses, poliovirus, other enteroviruses, mumps,herpes simplex, varicella-zoster, flaviviruses, or bunyaviruses.

Infections of the eye/orbit are commonly caused by the followingbacterial species: Staphylococcus aureus, Streptococcus pyogenes,Streptococcus pneumoniae, Streptococcus milleri, Escherichia coli,Bacillus cereus, Chlamydia trachomatis, Haemophilus influenza,Pseudomonas spp., Klebsiella spp., or Treponema pallidum; or viralpathogens: adenoviruses, herpes simplex, varicella-zoster, orcytomegalovirus.

Infections of the salivary glands are commonly caused by the followingbacterial species: Staphylococcus aureus, viridans streptococci (e.g.,Streptococcus salivarius, Streptococcus sanguis, Streptococcus mutans),Peptostreptococcus spp., or Bacteroides spp., or other oral anaerobes;or viral pathogens: mumps, influenza, enteroviruses, or rabies.

Infections of the mouth are commonly caused by the following bacterialspecies: Prevotella melaninogenicus, anaerobic streptococci, viridansstreptococci, Actinomyces spp., Peptostreptococcus spp., or Bacteroidesspp., or other oral anaerobes; or viral pathogens: herpes simplex,coxsackieviruses, or Epstein-Barr.

Infections of the tonsils are commonly caused by the following bacterialspecies: Streptococcus pyogenes, or Group C or G B-hemolyticstreptococci; or viral pathogens: rhinoviruses, influenza, coronavirus,adenovirus, parainfluenza, respiratory syncytial virus, or herpessimplex.

Infections of the sinuses are commonly caused by the following bacterialspecies: Streptococcus pneumoniae, Haemophilus influenza, Moraxellacatarrhalis, a-streptococci, anaerobic bacteria (e.g., Prevotella spp.),or Staphylococcus aureus; or viral pathogens: rhinoviruses, influenza,adenovirus, or parainfluenza.

Infections of the nasopharynx are commonly caused by the followingbacterial species: Streptococcus pyogenes, or Group C or G B-hemolyticstreptococci; or viral pathogens: rhinoviruses, influenza, coronavirus,adenovirus, parainfluenza, respiratory syncytial virus, or herpessimplex.

Infections of the thyroid are commonly caused by the following bacterialspecies: Staphylococcus aureus, Streptococcus pyogenes, or Streptococcuspneumoniae; or viral pathogens: mumps, or influenza.

Infections of the larynx are commonly caused by the following bacterialspecies: Mycoplasma pneumoniae, Chlamydophila pneumoniae, orStreptococcus pyogenes; or viral pathogens: rhinovirus, influenza,parainfluenza, adenovirus, corona virus, or human metapneumovirus.

Infections of the trachea are commonly caused by the following bacterialspecies: Mycoplasma pneumoniae; or viral pathogens: parainfluenza,influenza, respiratory syncytial virus, or adenovirus.

Infections of the bronchi are commonly caused by the following bacterialspecies: Mycoplasma pneumoniae, Chlamydophila pneumoniae, Bordetellapertussis, Streptococcus pneumoniae, or Haemophilus influenzae; or viralpathogens: influenza, adenovirus, rhinovirus, coronavirus,parainfluenza, respiratory syncytial virus, human metapneumovirus, orcoxsackievirus.

Infections of the lung are commonly caused by the following bacterialspecies: Streptococcus pneumoniae, Moraxella catarrhalis, Mycoplasmapneumoniae, Klebsiella pneumoniae, or Haemophilus influenza; or viralpathogens: influenza, adenovirus, respiratory syncytial virus, orparainfluenza.

Infections of the pleura are commonly caused by the following bacterialspecies: Staphylococcus aureus, Streptococcus pyogenes, Streptococcuspneumoniae, Haemophilus influenzae, Bacteroides fragilis, Prevotellaspp., Fusobacterium nucleatum, peptostreptococcus spp., or Mycobacteriumtuberculosis; or viral pathogens: influenza, adenovirus, respiratorysyncytial virus, or parainfluenza.

Infections of the mediastinum are commonly caused by the followingbacterial species: viridans streptococci, Peptococcus spp.,Peptostreptococcus spp., Bacteroides spp., Fusobacterium spp., orMycobacterium tuberculosis, or viral pathogens: measles, rubella,Epstein-Barr, or cytomegalovirus.

Infections of the heart are commonly caused by the following bacterialspecies: Streptococcus spp. (including S. mitior, S. bovis, S. sanguis,S. mutans, S. anginosus), Enterococcus spp., Staphylococcus spp.,Corynebacterium diptheriae, Clostridium perfringens, Neisseriameningitidis, or Salmonella spp.; or viral pathogens: enteroviruses,coxsackieviruses, echoviruses, poliovirus, adenovirus, mumps, rubeola,or influenza.

Infections of the esophagus are commonly caused by the followingbacterial species: Actinomyces spp., Mycobacterium avium, Mycobacteriumtuberculosis, or Streptococcus spp.; or viral pathogens:cytomegalovirus, herpes simplex, or varicella-zoster.

Infections of the stomach are commonly caused by the following bacterialspecies: Streptococcus pyogenes or Helicobacter pylori; or viralpathogens: cytomegalovirus, herpes simplex, Epstein-Barr, rotaviruses,noroviruses, or adenoviruses.

Infections of the small bowel are commonly caused by the followingbacterial species: Escherichia coli, Clostridium difficile, Bacteroidesfragilis, Bacteroides vulgatus, Bacteroides thetaiotaomicron,Clostridium perfnngens, Salmonella enteriditis, Yersinia enterocolitica,or Shigella flexneri; or viral pathogens: adenoviruses, astroviruses,caliciviruses, noroviruses, rotaviruses, or cytomegalovirus.

Infections of the colon/rectum are commonly caused by the followingbacterial species: Escherichia coli, Clostridium difficile, Bacteroidesfragilis, Bacteroides vulgatus, Bacteroides thetaiotaomicron,Clostridium perfringens, Salmonella enteriditis, Yersiniaenterocolitica, or Shigella flexneri; or viral pathogens: adenoviruses,astroviruses, caliciviruses, noroviruses, rotaviruses, orcytomegalovirus.

Infections of the anus are commonly caused by the following bacterialspecies: Streptococcus pyogenes, Bacteroides spp., Fusobacterium spp.,anaerobic streptococci, Clostridium spp., Escherichia coli, Enterobacterspp., Pseudomonas aeruginosa, or Treponema pallidum; or viral pathogens:herpes simplex.

Infections of the perineum are commonly caused by the followingbacterial species: Escherichia coli, Klebsiella spp., Enterococcus spp.,Bacteroides spp., Fusobacterium spp., Clostridium spp., Pseudomonasaeruginosa, anaerobic streptococci, Clostridium spp., or Enterobacterspp.; or viral pathogens: herpes simplex.

Infections of the liver are commonly caused by the following bacterialspecies: Escherichia coli, Klebsiella spp., Streptococcus (anginosusgroup), Enterococcus, spp. other viridans streptococci, or Bacteroidesspp.; or viral pathogens: hepatitis A, Epstein-Barr, herpes simplex,mumps, rubella, rubeola, varicella-zoster, coxsackieviruses, oradenovirus.

Infections of the gallbladder are commonly caused by the followingbacterial species: Escherichia coli, Klebsiella spp., Enterobacter spp.,enterococci, Bacteroides spp., Fusobacterium spp., Clostridium spp.,Salmonella enteriditis, Yersinia enterocolitica, or Shigella flexneri.

Infections of the biliary tract are commonly caused by the followingbacterial species: Escherichia coli, Klebsiella spp., Enterobacter spp.,enterococci, Bacteroides spp., Fusobacterium spp., Clostridium spp.,Salmonella enteriditis, Yersinia enterocolitica, or Shigella flexneri;or viral pathogens: hepatitis A, Epstein-Barr, herpes simplex, mumps,rubella, rubeola, varicella-zoster, cocsackieviruses, or adenovirus.

Infections of the pancreas are commonly caused by the followingbacterial species: Escherichia coli, Klebsiella spp., Enterococcus spp.,Pseudomonas spp., Staphylococcal spp., Mycoplasma spp., Salmonellatyphi, Leptospirosis spp., or Legionella spp.; or viral pathogens:mumps, coxsackievirus, hepatitis B, cytomegalovirus, herpes simplex 2,or varicella-zoster.

Infections of the spleen are commonly caused by the following bacterialspecies: Streptococcus spp., Staphylococcus spp., Salmonella spp.,Pseudomonas spp., Escherichia coli, or Enterococcus spp.; or viralpathogens: Epstein-Barr, cytomegalovirus, adenovirus, measles, rubella,coxsackieviruses, or varicella-zoster.

Infections of the adrenal gland are commonly caused by the followingbacterial species: Streptococcus spp., Staphylococcus spp., Salmonellaspp., Pseudomonas spp., Escherichia coli, or Enterococcus spp.; or viralpathogens: varicella-zoster.

Infections of the kidney are commonly caused by the following bacterialspecies: Escherichia coli, Proteus mirabilis, Proteus vulgatus,Providentia spp., Morganella spp., Enterococcus faecalis, or Pseudomonasaeruginosa; or viral pathogens: BK virus, or mumps.

Infections of the ureter are commonly caused by the following bacterialspecies: Escherichia coli, Proteus mirabilis, Proteus vulgatus,Providentia spp., Morganella spp., or Enterococcus spp.

Infections of the bladder are commonly caused by the following bacterialspecies: Escherichia coli, Proteus mirabilis, Proteus vulgatus,Providentia spp., Morganella spp., Enterococcus faecalis, orCorynebacterium jekeum; or viral pathogens: adenovirus, orcytomegalovirus.

Infections of the peritoneum are commonly caused by the followingbacterial species: Staphylococcus aureus, Streptococcus pyogenes,Streptococcus pneumonia, Escherichia coli, Klebsiella spp., Proteusspp., enterococci, Bacteroides fragilis, Prevotella melaninogenica,Peptococcus spp., Peptostreptococcus spp., Fusobacterium spp., orClostridium spp.

Infections of the retroperitoneal area are commonly caused by thefollowing bacterial species: Escherichia coli, or Staphylococcus aureus.

Infections of the prostate are commonly caused by the followingbacterial species: Escherichia coli, Klebsiella spp., Enterobacter spp.,Proteus mirabilis, enterococci spp., Pseudomonas spp., Corynebacteriumspp., or Neisseria gonorrhoeae; or viral pathogens: herpes simplex.

Infections of the testicle are commonly caused by the followingbacterial species: Escherichia coli, Klebsiella pneumoniae, Pseudomonasaeruginosa, Staphylococcus spp., Streptococcus spp., or Salmonellaenteriditis; or viral pathogens: mumps, coxsackievirus, or lymphocyticchoriomeningitis virus.

Infections of the penis are commonly caused by the following bacterialspecies: Staphylococcus aureus, Streptococcus pyogenes, Neisseriagonorrhoeae, or Treponema pallidum; or viral pathogens: herpes simplex.

Infections of the ovary/adnexae are commonly caused by the followingbacterial species: Neisseria gonorrhoeae, Chlamydia trachomatis,Gardenerella vaginalis, Prevotella spp., Bacteroides spp., Peptococcusspp. Streptococcus spp., or Escherichia coli.

Infections of the uterus are commonly caused by the following bacterialspecies: Neisseria gonorrhoeae, Chlamydia trachomatis, Gardenerellavaginalis, Prevotella spp., Bacteroides spp., Peptococcus spp.,Streptococcus spp., or Escherichia coli.

Infections of the cervix are commonly caused by the following bacterialspecies: Neisseria gonorrhoeae, Chlamydia trachomatis, or Treponemapallidum; or viral pathogens: herpes simplex.

Infections of the vagina are commonly caused by the following bacterialspecies: Gardenerella vaginalis, Prevotella spp., Bacteroides spp.,peptococci spp., Escherichia coli, Neisseria gonorrhoeae, ChlamydiaTrachomatis, or Treponema pallidum; or viral pathogens: herpes simplex.

Infections of the vulva are commonly caused by the following bacterialspecies: Staphylococcus aureus, Streptococcus pyogenes, or Treponemapallidum; or viral pathogens: herpes simplex.

Bacterial Strains/Viral Subtypes

It will be understood by a skilled person in the art that bacterialspecies are classified operationally as collections of similar strains(which generally refers to groups of presumed common ancestry withidentifiable physiological but usually not morphological distinctions,and which may be identified using serological techniques againstbacterial surface antigens). Thus, each bacterial species (e.g.,Streptococcus pneumoniae) has numerous strains (or serotypes), which maydiffer in their ability to cause infection or differ in their ability tocause infection in a particular organ/site. For example, although thereare at least 90 serotypes of Streptococcus pneumoniae, serotypes 1, 3,4, 7, 8, and 12 are most frequently responsible for pneumococcal diseasein humans.

As a second example, certain strains of Escherichia coli, referred to asextraintestinal pathogenic E. coli (ExPEC), are more likely to causeurinary tract infection or other extraintestinal infections such asneonatal meningitis, whereas other strains, including enterotoxigenic E.coli (ETEC), enteropathogenic E. coli (EPEC), enterohemorrhagic E. coli(EHEC), Shiga toxin-producing E. coli (STEC), enteroaggregative E. coli(EAEC), enteroinvasive E. coli (EIEC) and diffuse adhering E. coli(DAEC) are more likely to cause gastrointestinal infection/diarrhea.Even among the sub-category of ExPEC strains, specific virulence factors(e.g., production of type-1 fimbriae) enable certain strains to be morecapable of causing infection of the bladder, while other virulencefactors (e.g., production of P fimbriae) enable other strains to be morecapable of causing infection in the kidneys. In accordance with thepresent invention, an ExPEC strain(s) that is more likely to causeinfection in the bladder may be chosen for a formulation to targetbladder cancer, whereas an ExPEC strain(s) that is more likely to causeinfection in the kidney may be chosen for a formulation to target kidneycancer. Likewise, one or more of an ETEC, EPEC, EHEC, STEC, EAEC, EIECor DAEC strains of E. coli (i.e., strains that cause colon infection),may be chosen for a formulation to treat colon cancer.

Similarly, there may be numerous subtypes of specific viruses. Forexample, there are three types of influenza viruses, influenza A,influenza B and influenza C, which differ in epidemiology, host rangeand clinical characteristics. For example, influenza A is more likely tobe associated with viral lung infection, whereas influenza B is morelikely to be associated with myositis (i.e., muscle infection).Furthermore, each of these three types of influenza virus have numeroussubtypes, which also may differ in epidemiology, host range and clinicalcharacteristics. In accordance with the present invention, one maychoose an influenza A subtype most commonly associated with lunginfection to target lung cancer, whereas one may choose an influenza Bstrain most commonly associated with myositis to treat cancer of themuscle/soft tissues.

It is understood that a clinical microbiologist skilled in the art wouldtherefore be able to select, based on the present disclosure and thebody of art relating to bacterial strains for each species of bacteria(and viral subtypes for each type of virus), the strains of a particularbacterial species (or subtype of a particular virus) to target aspecific organ or tissue.

Bacterial Compositions, Dosages, and Administration

The compositions of the invention include antigens of pathogenicmicrobial (bacterial or viral) species that are pathogenic in a specifictissue or organ. The compositions may include whole bacterial species,or may include extracts or preparations of the pathogenic bacterialspecies of the invention, such as cell wall or cell membrane extracts,or whole cells, or exotoxins, or whole cells and exotoxins. Thecompositions may also include one or more isolated antigens from one ormore of the pathogenic bacterial species of the invention; in someembodiments, such compositions may be useful in situations where it maybe necessary to precisely administer a specific dose of a particularantigen, or may be useful if administering a whole bacterial species orcomponents thereof (e.g., toxins) may be harmful. Pathogenic bacterialspecies may be available commercially (from, for example, ATCC(Manassas, Va., USA), or may be clinical isolates from subjects having abacterial infection of a tissue or organ (e.g., pneumonia).

The microbial compositions of the invention can be provided alone or incombination with other compounds (for example, nucleic acid molecules,small molecules, peptides, or peptide analogues), in the presence of aliposome, an adjuvant, or any pharmaceutically acceptable carrier, in aform suitable for administration to mammals, for example, humans. Asused herein “pharmaceutically acceptable carrier” or “excipient”includes any and all solvents, dispersion media, coatings, antibacterialand antifungal agents, isotonic and absorption delaying agents, and thelike that are physiologically compatible. The carrier can be suitablefor any appropriate form of administration, including subcutaneous,intradermal, intravenous, parenteral, intraperitoneal, intramuscular,sublingual, inhalational, intratumoral or oral administration.Pharmaceutically acceptable carriers include sterile aqueous solutionsor dispersions and sterile powders for the extemporaneous preparation ofsterile injectable solutions or dispersion. The use of such media andagents for pharmaceutically active substances is well known in the art.Except insofar as any conventional media or agent is incompatible withthe active compound (i.e., the specific bacteria, bacterial antigens, orcompositions thereof of the invention), use thereof in thepharmaceutical compositions of the invention is contemplated.Supplementary active compounds can also be incorporated into thecompositions.

If desired, treatment with bacterial antigens according to the inventionmay be combined with more traditional and existing therapies for cancer,such as chemotherapy, radiation therapy, surgery, etc., or with anyother therapy intended to stimulate the immune system, reduceinflammation or otherwise benefit the subject, such as nutrients,vitamins and supplements. For example, vitamin A, vitamin D, vitamin E,vitamin C, vitamin B complex, selenium, zinc, co-enzyme Q10, betacarotene, fish oil, curcumin, green tea, bromelain, resveratrol, groundflaxseed, garlic, lycopene, milk thistle, melatonin, other antioxidants,cimetidine, indomethacin, or COX-2 Inhibitors (e.g., Celebrex™[celecoxib] or Vioxx™ [rofecoxib]) may be also be administered to thesubject.

Conventional pharmaceutical practice may be employed to provide suitableformulations or compositions to administer the compounds to subjectssuffering from a cancer. Any appropriate route of administration may beemployed, for example, parenteral, intravenous, intradermal,subcutaneous, intramuscular, intracranial, intraorbital, ophthalmic,intraventricular, intracapsular, intraspinal, intrathecal,intracisternal, intraperitoneal, intranasal, inhalational, aerosol,topical, intratumoral, sublingual or oral administration. Therapeuticformulations may be in the form of liquid solutions or suspensions; fororal administration, formulations may be in the form of tablets orcapsules; for intranasal formulations, in the form of powders, nasaldrops, or aerosols; and for sublingual formulations, in the form ofdrops, aerosols or tablets.

Methods well known in the art for making formulations are found in, forexample, “Remington's Pharmaceutical Sciences” (20th edition), ed. A.Gennaro, 2000, Mack Publishing Company, Easton, Pa. Formulations forparenteral administration may, for example, contain excipients, sterilewater, or saline, polyalkylene glycols such as polyethylene glycol, oilsof vegetable origin, or hydrogenated napthalenes. Biocompatible,biodegradable lactide polymer, lactide/glycolide copolymer, orpolyoxyethylene-polyoxypropylene copolymers may be used to control therelease of the compounds. Other potentially useful parenteral deliverysystems for include ethylene-vinyl acetate copolymer particles, osmoticpumps, implantable infusion systems, and liposomes. Formulations forinhalation may contain excipients, for example, lactose, or may beaqueous solutions containing, for example, polyoxyethylene-9-laurylether, glycocholate and deoxycholate, or may be oily solutions foradministration in the form of nasal drops, or as a gel. For therapeuticor prophylactic compositions, the pathogenic bacterial species areadministered to an individual in an amount effective to stop or slowprogression or metastasis of the cancer, or to increase survival of thesubject (relative to, for example, prognoses derived from the SEERdatabase) depending on the disorder.

An “effective amount” of a pathogenic microbial species or antigenthereof according to the invention includes a therapeutically effectiveamount or a prophylactically effective amount. A “therapeuticallyeffective amount” refers to an amount effective, at dosages and forperiods of time necessary, to achieve the desired therapeutic result,such as reduction or elimination of the cancer cells or tumors,prevention of carcinogenic processes, slowing the growth of the tumour,or an increase in survival time beyond that which is expected using forexample the SEER database. A therapeutically effective amount of apathogenic microbial (bacterial or viral) species or antigen(s) thereofmay vary according to factors such as the disease state, age, sex, andweight of the individual, and the ability of the compound to elicit adesired response in the individual. Dosage regimens may be adjusted toprovide the optimum therapeutic response. A therapeutically effectiveamount may also be one in which any toxic or detrimental effects of thepathogenic bacterial species or virus or antigen thereof are outweighedby the therapeutically beneficial effects. A “prophylactically effectiveamount” refers to an amount effective, at dosages and for periods oftime necessary, to achieve the desired prophylactic result, such asprevention of cancer, prevention of metastasis, slowing the growth ofthe tumour, reduction or elimination of the cancer cells, tissues,organs, or tumors, or an increase in survival time beyond that which isexpected using for example the SEER database. Typically, a prophylacticdose is used in subjects prior to or at an earlier stage of cancer, sothat a prophylactically effective amount may be less than atherapeutically effective amount.

For administration by subcutaneous or intradermal injection, anexemplary range for therapeutically or prophylactically effectiveamounts of one or more pathogenic bacterial species may be about 1million to 100,000 million organisms per ml, or may be 100 million to7000 million organisms per ml, or may be 500 million to 6000 millionorganisms per ml, or may be 1000 million to 5000 million organisms perml, or may be 2000 million to 4000 million organisms per ml, or anyinteger within these ranges. The total concentration of bacteria per mlmay range from 1 million to 100,000 million organisms per ml, or may be50 million to 7000 million organisms per ml, or may be 100 million to6000 million organisms per ml, or may be 500 million to 5000 millionorganisms per ml, or may be 1000 million to 4000 million organisms perml, or any integer within these ranges. The range for therapeutically orprophylactically effective amounts of antigens of a pathogenic bacterialspecies may be any integer from 0.1 nM-0.1 M, 0.1 nM-0.05M, 0.05 nM-15μM or 0.01 nM-10 μM.

It is to be noted that dosage concentrations and ranges may vary withthe severity of the condition to be alleviated, or may vary with thesubject's immune response. In general, the goal is to achieve anadequate immune response. For administration by subcutaneous orintradermal infection, the extent of an immune response may bedetermined, for example, by size of delayed local immune skin reactionat the site of injection (e.g., from 0.25 inch to 4 inch diameter). Thedose required to achieve an appropriate immune response may varydepending on the individual (and their immune system) and the responsedesired. Standardized dosages may also be used. In the context ofsubcutaneous or intradermal administration, if the goal is to achieve a2 inch local skin reaction, the total bacterial composition dose may,for example, range from 2 million bacteria (e.g., 0.001 ml of a vaccinewith a concentration of 2,000 million organisms per ml) to more than20,000 million bacteria (e.g., 1 ml of a vaccine with a concentration of20,000 million organisms per ml). The concentrations of individualbacterial species or antigens thereof within a composition may also beconsidered. For example, if the concentration of one particularpathogenic bacterial species, cell size of that species or antigenicload thereof is much higher relative to the other pathogenic bacterialspecies in the vaccine, then the local immune skin reaction of anindividual may be likely due to its response to this specific bacterialspecies. In some embodiments, the immune system of an individual mayrespond more strongly to one bacterial species within a composition thananother, depending for example on past history of exposure to infectionby a particular species, so the dosage or composition may be adjustedaccordingly for that individual. However, in some embodiments detailedherein, an immune response will not be monitored by way of a skinreaction. For example, in some mouse models utilized herein, theeffective treatment of such animals with antigenic compositions may notresult in corresponding skin reactions. A person skilled in the art willunderstand that there are alternate ways in which an immune response canbe monitored beside relying on the presence or absence of a skinreaction.

For any particular subject, the timing and dose of treatments may beadjusted over time (e.g., timing may be daily, every other day, weekly,monthly) according to the individual need and the professional judgmentof the person administering or supervising the administration of thecompositions. For example, in the context of subcutaneous or intradermaladministration, the compositions may be administered every second day.An initial dose of approximately 0.05 ml may be administeredsubcutaneously, followed by increases from 0.01-0.02 ml every second dayuntil an adequate skin reaction is achieved at the injection site (forexample, a 1 inch to 2 inch diameter delayed reaction of visible rednessat the injection site). Once this adequate immune reaction is achieved,this dosing is continued as a maintenance dose. The maintenance dose maybe adjusted from time to time to achieve the desired visible skinreaction (inflammation) at the injection site. Dosing may be for adosage duration, for example of at least 1 week, 2 weeks, 2 months, 6months, 1, 2, 3, 4, or 5 years or longer.

Oral dosages may for example range from 10 million to 1,000,000 millionorganisms per dose, comprising antigenic determinants of one or morespecies. Oral dosages may be given, for example, from 4 times per day,daily or weekly. Dosing may be for a dosage duration, for example of atleast 1 week, 2 weeks, 2 months, 6 months, 1, 2, 3, 4, or 5 years orlonger.

In some embodiments, the invention may include antigenic compositionsadministered sublingually or by inhalation, or administered to one ormore epithelial tissues (i.e., skin by intradermal or subcutaneousinjection; lung epithelium by inhalation; gastrointestinal mucosa byoral ingestion; mouth mucosa by sublingual administration)simultaneously or sequentially. Accordingly, in some embodiments theantigenic compositions of the invention are administered so as toprovoke an immune response in an epithelial tissue. In some embodiments,one or more epithelial routes of administration may be combined with oneor more additional routes of administration, such as intratumoral,intramuscular or intravenous administration.

In various aspects of the invention, the antigenic compositions that areadministered to a patient may be characterized as having an antigenicsignature, i.e., a combination of antigens or epitopes that aresufficiently specific that the antigenic composition is capable ofeliciting an immune response that is specific to a particular pathogen,such as an adaptive immune response. A surprising and unexpected aspectof the invention is that the non-adaptive or non-specific activation ofthe immune response that is mediated by these specific antigeniccompositions is effective to treat cancers situated in the tissues inwhich the particular pathogen is pathogenic.

Routes of administration and dosage ranges set forth herein areexemplary only and do not limit the route of administration and dosageranges that may be selected by medical practitioners. The amount ofactive compound (e.g., pathogenic bacterial species or viruses orantigens thereof) in the composition may vary according to factors suchas the disease state, age, sex, and weight of the individual. Dosageregimens may be adjusted to provide the optimum therapeutic response.For example, a single bolus may be administered, several divided dosesmay be administered over time or the dose may be proportionally reducedor increased as indicated by the exigencies of the therapeuticsituation. It may be advantageous to formulate parenteral compositionsin dosage unit form for ease of administration and uniformity of dosage.

In the case of antigenic formulations (analogous to a vaccine), animmunogenically effective amount of a compound of the invention can beprovided, alone or in combination with other compounds, with animmunological adjuvant. The compound may also be linked with a carriermolecule, such as bovine serum albumin or keyhole limpet hemocyanin toenhance immunogenicity. An antigenic composition (“vaccine”) is acomposition that includes materials that elicit a desired immuneresponse. An antigenic composition may select, activate or expand,without limitation: memory B, T cells, neutrophils, monocytes ormacrophages of the immune system to, for example, reduce or eliminatethe growth or proliferation of cancerous cells or tissue. In someembodiments, the specific pathogenic microbe, virus, viral antigens,bacteria, bacterial antigens, or compositions thereof of the inventionare capable of eliciting the desired immune response in the absence ofany other agent, and may therefore be considered to be an antigeniccomposition. In some embodiments, an antigenic composition includes asuitable carrier, such as an adjuvant, which is an agent that acts in anon-specific manner to increase the immune response to a specificantigen, or to a group of antigens, enabling the reduction of thequantity of antigen in any given vaccine dose, or the reduction of thefrequency of dosage required to generate the desired immune response. Abacterial antigenic composition may include live or dead bacteriacapable of inducing an immune response against antigenic determinantsnormally associated with the bacteria. In some embodiments, an antigeniccomposition may include live bacteria that are of less virulent strains(attenuated), and therefore cause a less severe infection. In someembodiments the antigenic composition may include live, attenuated ordead viruses capable of inducing an immune response against antigenicdeterminants normally associated with the virus.

An antigenic composition comprising killed bacteria for administrationby injection may be made as follows. The bacteria may be grown insuitable media, and washed with physiological salt solution. Thebacteria may then be centrifuged, resuspended in saline solution, andkilled with heat. The suspensions may be standardized by directmicroscopic count, mixed in required amounts, and stored in appropriatecontainers, which may be tested for safety, shelf life, and sterility inan approved manner. In addition to the pathogenic bacterial speciesand/or antigens thereof, a killed bacterial vaccine suitable foradministration to humans may include 0.4% phenol preservative and/or0.9% sodium chloride. The bacterial vaccine may also include traceamounts of brain heart infusion (beef), peptones, yeast extract, agar,sheep blood, dextrose, sodium phosphate and/or other media components.

In some embodiments, the bacterial vaccine may be used in tablet orcapsule form or drops for oral ingestion, as an aerosol for inhalation,or as drops, aerosol or tablet form for sublingual administration.

In antigenic compositions comprising bacteria, the concentrations ofspecific bacterial species in compositions for subcutaneous orintradermal injection may be about 1 million to 100,000 millionorganisms per ml, or may be 100 million to 7000 million organisms perml, or may be 500 million to 6000 million organisms per ml, or may be1000 million to 5000 million organisms per ml, or may be 2000 million to4000 million organisms per ml, or any integer within these ranges. Thetotal concentration of bacteria per ml may range from 1 million to100,000 million organisms per ml, or may be 50 million to 7000 millionorganisms per ml, or may be 100 million to 6000 million organisms perml, or may be 500 million to 5000 million organisms per ml, or may be1000 million to 4000 million organisms per ml, or any integer withinthese ranges.

In some embodiments, a selected killed bacterial vaccine for cancer ofthe lung tissue would include the common bacterial lung pathogens, andmay for example be:

bacteria per ml Streptococcus pneumoniae 600 million Haemophilusinfluenzae 400 million Moraxella catarrhalis 400 million Mycoplasmapneumoniae 300 million Klebsiella pneumoniae 300 million total: 2,000million  or alternatively:

bacteria per ml Streptococcus pneumoniae 600 million Haemophilusinfluenzae 300 million Moraxella catarrhalis 300 million Mycoplasmapneumoniae 400 million Klebsiella pneumoniae 400 million total: 2,000million  In some selected embodiments, a selected killed bacterial vaccine forcancer of the lung tissue would include only more common bacterial lungpathogens, and may for example be:

bacteria per ml Streptococcus pneumoniae 800 million Haemophilusinfluenzae 600 million Moraxella catarrhalis 600 million total: 2,000million  or alternatively:

bacteria per ml Streptococcus pneumoniae 800 million Mycoplasmapneumoniae 600 million Klebsiella pneumoniae 600 million total: 2,000million  

In further selected embodiments, a selected killed bacterial vaccine forcancer of the lung tissue would include only the most common bacteriallung pathogen, and may be:

bacteria per ml Streptococcus pneumoniae 2,000 million total: 2,000millionor

bacteria per ml Klebsiella pneumoniae 2,000 million total: 2,000 millionor

bacteria per ml Mycoplasma pneumoniae 2,000 million total: 2,000 million

In some embodiments, an antigenic microbial composition for treatingcancer at a particular site (e.g., cancer of the lung tissue) mayinclude pathogenic microbes that commonly, more commonly, or mostcommonly cause infection in that tissue or organ (e.g., infection in thelung tissue i.e., pneumonia).

In general, the pathogenic bacterial species and antigens thereof of theinvention should be used without causing substantial toxicity. Toxicityof the compounds of the invention can be determined using standardtechniques, for example, by testing in cell cultures or experimentalanimals and determining the therapeutic index, i.e., the ratio betweenthe LD50 (the dose lethal to 50% of the population) and the LD100 (thedose lethal to 100% of the population).

In some aspects, the invention involves the use of an anti-inflammatoryin conjunction with vaccinations. In these embodiments, a wide varietyof anti-inflammatory treatments may be employed, including effectiveamounts of non-steroidal anti-inflammatory drugs (NSAIDs), including butnot limited to: diclofenac potassium, diclofenac sodium, etodolac,indomethicin, ketorolac tromethamine, sulindac, tometin sodium,celecoxib, meloxicam, valdecoxib, floctafenine, mefenamic acid,nabumetone, meloxicam, piroxicam, tenoxicam, fenoprofen calcium,flubiprofen, ibuprofen, ketoprofen, naproxen, naproxen sodium,oxaprozin, tiaprofenic acid, acetylsalicylic acid, diflunisal, cholinemagnesium trisalicylate, choline salicylate, triethanolamine salicylate,COX1 inhibitors, COX2 inhibitors (e.g., Vioxx™, and Celebrex™). Avariety of herbs and natural health products may also be used to provideanti-inflammatory treatment, including but not limited to: green tea,fish oil, vitamin D, antioxidant vitamins and minerals (e.g., Bcarotene, vitamin A, vitamin C, vitamin D, vitamin E, co-enzyme Q10,selenium, etc.), resveratrol, turmeric, bromelain, boswellia, feverfew,quercetin, ginger, rosemary, oregano, cayenne, clove, nutmeg,willowbark. Alternative anti-inflammatory modalities may also includelifestyle modifications, such as: exercise, weight loss, smokingcessation, stress reduction, seeking social support, treatment ofdepression, stress management, abdominal breath work and dietary change(such as adopting a mediterranean diet, a low glycemic diet, eatingnon-charred foods, including foods having omega-3 fatty acids).

As detailed herein and in an aspect of the invention, a method ofcomparing immune responses is provided. The method involvesadministering to an animal having an organ or tissue a medicament havingan antigenic composition, as defined herein. The antigenic compositionmay have antigenic determinants selected or formulated so that togetherthe antigenic determinants are specific for at least one microbialpathogen that is pathogenic in the organ or tissue, extracting aquantifiable immune sample from the organ or tissue, measuring acharacteristic of the immune response in the organ or tissue in thequantifiable immune sample following the administration of themedicament, and, comparing the characteristic of the immune response inthe quantifiable immune sample to a corresponding characteristic of theimmune response in a reference immune sample obtained from acorresponding organ or tissue. As used herein, an immune sample wouldcontain sufficient biological material to determine a characteristic ofan immune response. As used herein, a “characteristic” of an immuneresponse can include, without limitation, the particular number of aparticular immune cell type (e.g., macrophage), or a particular cellularmarker (e.g., upregulation of an integrin) or gene product (e.g., acytokine). The foregoing is provided as an example and is non-limiting.

Optionally, the reference immune sample may be obtained from thecorresponding organ or tissue in the animal prior to the step ofadministering the medicament. In another aspect, the reference immunesample may be obtained from the corresponding organ or tissue in asecond animal such that it is specifically contemplated that at leasttwo animals (i.e., an animal from which a reference immune sample isobtained and a second animal from which a quantifiable immune sample)could be used in the methods described herein. Optionally, the animalmay have a cancer situated in the organ or tissue.

Comparing the characteristic of the immune response may involvecomparing, in the quantifiable and reference immune samples, anindication of the numbers of any one or more of the following cells asthese cells are known to those skilled in the art: inflammatorymonocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells, CD11c+ MHCclass II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Optionally,the macrophages may include any one or more of the following: M1-likemacrophages or M2-like macrophages.

Those persons skilled in the art will appreciate that macrophages can bedefined as either “M1-like macrophages” or “M2-like macrophages”. Forexample, M1-like macrophages are generally understood by those personsskilled in the art to promote a Th1 CD4+ T cell-mediated response (see,for e.g., Biswas and Mantovani (2010), Nature Immunology 10:889-96).Moreover, M1-like macrophages are generally understood to have efficientantigen presentation capacity, and to be proficient at killingintracellular pathogens (for e.g., viruses). Moreover, M1-likemacrophages are generally understood to be proficient, at least ascompared with M2-like macrophages, in playing an immunological role intumour destruction. Those skilled in the art will appreciate that thereare numerous biological markers which can be employed to differentiatebetween M1-like macrophages and M2-like macrophages. For example, and asdetailed herein, the expression of Nos2 is generally understood tocorrelate with an M1-like macrophage as compared with an M2-likemacrophage (see, for e.g., Laskin et al. (2010) Annual Rev. Pharmacol.Toxicol. 51: 267-288). Further, and for example, M1-like macrophages aregenerally understood to produce IL-12 and to be effectively activated byIFN-γ through the IFN— γR (Biswas and Mantovain, supra).

In contrast to M1-like macrophages, those persons skilled in the artwill generally understand that M2-like macrophages promote a Th2 CD4+ Tcell-mediated response (see, generally: Biswas and Mantovani (2010),Nature Immunology 10:889-96). Moreover, M2-like macrophages aregenerally understood to be effective and encapsulating and clearingextracellular parasites etc. Further, and in comparison to M1-likemacrophages, M2-like macrophages are generally understood by thosepersons skilled in the art as playing a more significant role inimmunoregulation both with respect to T_(reg) and B cells (Biswas andMantovain, supra). Those persons skilled in the art will appreciate thatthere are numerous biological markers which can be employed todifferentiate between M2-like macrophages and M1-like macrophages. Forexample, and as described herein, a diminished expression of Nos2 willgenerally be understood to correlate with M2-like macrophages ascompared with higher expression being generally found in M1-likemacrophages. Further, and as detailed in experiments herein, theexpression of CD206 is generally understood as correlating with M2-likemacrophages (see, for e.g., Choi et al. (2010) Gastroenterology 138(7)2399-409). Further, and as detailed in experiments herein, theexpression of F4/80 is generally understood to correlate with M2-likemacrophages. Further, and for example, M2-like macrophages are generallyunderstood to be effectively activated by IL-4 or by IL-13 throughIL-4Rα (Biswas and Mantovain, supra).

Further, comparing the characteristic of the immune response may involvecomparing a shift in an activation state of macrophages. The shift inthe activation state of macrophages may optionally be characterized as ashift from M2-like macrophages to M1-like macrophages or vice versa.Those persons skilled in the art will appreciate that there are numerousbiological markers that can be employed to monitor the activation ofmacrophages. As detailed herein, those skilled in the art willappreciate that defining a macrophage as being activated towards eithera M1-like phenotype or a M2-like phenotype can be accomplished bychoosing markers that are known to associate with either of therespective phenotypes described herein. Diseases which have beenassociated with M1 and M2 macrophages include at least the following:atherosclerosis (see, for e.g., Hirata et al. (2011) J. Am. Coll.Cardiol. 58(3): 248-255), allergic asthma (see, for e.g., Moreira andHogaboam (2011) J. Interferon. Cytokine Res. 31(6): 485-91), autoimmuneprostatitis (see, for e.g., Zhang and Schluesener (2011) Prostate),colitis (see, for e.g., Waddell et al. (2011) J. Immunol. 186(10):5993-6003), COPD (see, for e.g., Kunz et al. (2011) Respir. Res. 22:34), glomerulonephritis (see, for e.g., Fujita et al. (2010) Am. J.Pathol. 177(3): 1143-54), inflammatory bowel disease (see, for e.g.,Wendelsdorf et al. (2010) J. Theor. Biol. 264(4): 1225-39), chronic lunginflammation (see, for e.g., Redente et al. (2010) J. Leukoc. BIol.88(1): 159-68), steatohepatitis (see, for e.g., Rensen et al. (2009) Am.J. Pathol. 175(4): 1473-82), pancreatitis (see, for e.g., Gea-Sorli andClosa (2009) BMC Immunol. 31: 42), mycocarditis (see, for e.g., Li etal. (2009) Circ. Res. 105(4): 353-64), liver fibrosis (see, for e.g.,Heymann et al. (2009) Inflamm. Allergy Drug Targets 8(4): 307-18),cystic fibrosis (see, for e.g., Meyer et al. (2009) Am. J. Respir. CellMol. Biol. 41(5): 590-602), inflammatory renal disease (see, for e.g.,Wang et al. (2007) Kidney Int. 72(3): 290-299), and silicosis (see, fore.g., Misson et al. (2004) J. Leukoc. Biol. 76(5): 926-232).

Optionally, comparing the characteristic of the immune response mayinvolve identifying, in the quantifiable and reference immune samples,cellular markers on any one or more of the following cells as they arecommonly understood to those persons skilled in the art: inflammatorymonocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells, CD11c+ MHCclass II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Themacrophages may include any one or more of the following: M1-likemacrophages or M2-like macrophages. A person skilled in the art willappreciate that there are numerous cell markers (both extracellular andintracellular) that can be selected which can identify an immuneresponse. For example, as described herein, the marker CD206 isgenerally understood as correlating with M2-like macrophages (see, fore.g., Choi et al. (2010) Gastroenterology 138(7) 2399-409).

Optionally, comparing the characteristic of the immune response mayinvolve identifying, in the quantifiable and reference immune samples,cytokines produced by any one or more of the following cells as they arecommonly understood to those persons skilled in the art: inflammatorymonocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells, CD11c+ MHCclass II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Those personsskilled in the art will appreciate that cytokines refer to smallcell-signalling protein molecules and that there are numerous cytokinesknown in the art. For example, cytokines have been grouped into type 1and type 2 classifications based on their role in immunologicalresponses. Common type 1 cytokines include IFN-γ and TGF-β. Common type2 cytokines include, but are not limited to IL-4 and IL-13. Cytokinescan be detected by numerous methodologies known to those persons skilledin the art. For example, and as detailed herein, ELISA experiments wereutilized to determine cytokine production from lung tissue (see, fore.g., FIG. 27).

As detailed herein, the macrophages may include any one or more of thefollowing: M1-like macrophages or M2-like macrophages as has beendefined herein. Optionally, the cytokines are produced as a result of ashift in an activation state of the macrophages. Optionally, themacrophages shift from being M2-like macrophages to being M1-likemacrophages. Further and optionally, the macrophages shift from beingM1-like macrophages to being M2-like macrophages.

Optionally, comparing the characteristic of the immune response mayinvolve identifying, in the quantifiable and reference immune samples,differential gene expression produced by any one or more of thefollowing cells as they are commonly understood to those persons skilledin the art: inflammatory monocytes, macrophages, CD11 b+Gr-1+ cells,dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells,or NK cells. The macrophages may include any one or more of thefollowing: M1-like macrophages or M2-like macrophages. The term“differential gene expression” is understood to mean an appreciabledifference between the expression of a particular gene of interest fromat least two experimental conditions. For example, if under a firstexperimental condition a particular gene has a defined expression levelas defined by gene expression methods used by those persons skilled inthe art and if under a second experimental condition the same gene hasan appreciable difference in its expression level, then there isdifferential expression of the gene of interest. Those persons skilledin the art will understand that there are numerous methodologies withwhich to detect differential gene expression. For example, commerciallyavailable quantitative PCR techniques can be used as detailed hereinwith respect to determining the relative Nos2/Arg1 ratios (see, fore.g., FIG. 29). Optionally, the differential gene expression is producedas a result of a shift in an activation state of the macrophages.Optionally, macrophages may shift from being M2-like macrophages tobeing M1-like macrophages as those terms have been defined herein.

In another embodiment, the medicament may be administered at anadministration site in successive doses given at a dosage interval ofbetween one hour and one month, over a dosage duration of at least oneweek. Optionally, the medicament may be administered intradermally orsubcutaneously. Optionally, the medicament may be administered in a doseso that each dose is effective to cause a visible localized inflammatoryimmune response at the administration site. Optionally, the medicamentmay be administered so that visible localized inflammation at theadministration site occurs within 1 to 48 hours. However, a visiblelocalized inflammatory immune response may not always be present in allcircumstances despite an immune response being initiated. Those skilledin the art will appreciate that there are other methods by which themounting of an immune response can be monitored. For example, theprofile (and relative change in characterization) of immune cells from asubject undergoing an immune reaction can be compared with those from asubject that is not undergoing an immune reaction.

Further and optionally with respect to the methods disclosed herein, theanimal may be a mammal. Optionally, the animal may be a human or amouse. The foregoing are provided as examples and are not meant to belimiting.

In another aspect, a method of selecting a therapeutic preparationsuitable for treating an individual for a cancer in a specific organ ortissue is provided. The method involves providing an animal having acancer situated in a specific organ or tissue, providing a testpreparation having one or more antigenic determinants of a microbialpathogen which is pathogenic in the corresponding specific organ ortissue in a healthy individual, measuring a characteristic of the immuneresponse in a reference immune sample obtained from the organ or tissueof the animal, administering the test preparation to the animal,measuring a characteristic of the immune response in a quantifiableimmune sample obtained from a corresponding organ or tissue of theanimal, comparing the characteristic of the immune response in the inthe reference and quantifiable immune samples, and treating an enhancedcharacteristic of the immune response in the quantifiable immune samplecompared to the reference immune sample as an indication of thesuitability of the test preparation as a therapeutic preparation.Optionally, the animal is sacrificed before the quantifiable immunesample has been obtained.

Optionally, comparing the characteristic of the immune response mayinvolve comparing, in the quantifiable and reference immune samples, anindication of the numbers of any one or more of the following cells asthey are commonly understood to those persons skilled in the art:inflammatory monocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells,CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells.Optionally, the macrophages may include any one or more of thefollowing: M1-like macrophages or M2-like macrophages as those termshave been defined herein. Optionally, comparing the characteristic ofthe immune response may involve comparing a shift in an activation stateof macrophages. Optionally, the macrophages may shift from being M2-likemacrophages to being M1-like macrophages. Further and optionally, themacrophages may shift from being M1-like macrophages to being M2-likemacrophages.

Optionally, comparing the characteristic of the immune response mayinvolve identifying, in the quantifiable and reference immune samples,cellular markers on any one or more of the following cells as they arecommonly understood to those persons skilled in the art: inflammatorymonocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells, CD11c+ MHCclass II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Optionally,the macrophages may include any one or more of the following: M1-likemacrophages or M2-like macrophages as those terms have been definedherein.

Optionally, comparing the characteristic of the immune response mayinvolve identifying, in the quantifiable and reference immune samples,cytokines produced by any one or more of the following cells:inflammatory monocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells,CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Themacrophages may include any one or more of the following: M1-likemacrophages or M2-like macrophages as those terms have been definedherein. Optionally, the cytokines are produced as a result of a shift inan activate state of the macrophages. Optionally, the macrophages mayshift from being M2-like macrophages to being M1-like macrophages.

Further and optionally, comparing the characteristic of the immuneresponse may involve identifying, in the quantifiable and referenceimmune samples, differential gene expression produced by any one or moreof the following cells: inflammatory monocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ Tcells, CD8+ T cells, or NK cells. Optionally, the macrophages mayinclude any one or more of the following: M1-like macrophages or M2-likemacrophages as those terms have been defined herein. Optionally, thedifferential gene expression may be produced as a result of a shift inan activation state of the macrophages. Optionally, the macrophages mayshift from being M2-like macrophages to being M1-like macrophages.Further and optionally, the macrophages may shift from being M1-likemacrophages to being M2-like macrophages.

In another aspect, a method of selectively targeting an immune responseto a cancerous tissue or an organ in a human subject is provided. Themethod involves administering to the subject a medicament having aneffective amount of a microbial pathogen antigenic composition, whereinthe microbial pathogen may be pathogenic in the specific cancerous organor tissue of the subject and the antigenic composition comprisesantigenic determinants that together are specific for the microbialpathogen. Optionally, the antigenic composition may include a wholekilled bacterial cell composition. Optionally, the medicament may beadministered to the subject in an amount and for a time that iseffective to up-regulate an immune response in the cancerous organ ortissue of the subject. Optionally, the method may further involvemeasuring a characteristic of the immune response.

In another aspect, a method for treating a human subject for a cancersituated in a tissue or an organ is provided. The method involvesadministering to the subject a medicament having an effective amount ofa microbial pathogen antigenic composition comprising a whole killedbacterial cell composition, wherein the microbial pathogen is pathogenicin the specific organ or tissue of the subject within which the canceris situated. The medicament may be administered to the subject in anamount and for a time that is effective to modulate an immune response.Optionally, the modulation of the immune response may involve a shift inthe activation state of macrophages. Optionally, the modulation of theimmune response may involve shifting from a M2-like macrophage responseto a M1-like macrophage response. The modulation of the immune responsesmay involve shifting from a M1-like macrophage response to a M2-likemacrophage response. Optionally, the method may further involvemeasuring a characteristic of the immune response.

Optionally, comparing the characteristic of the immune response mayinvolve comparing, in the quantifiable and reference immune samples, anindication of the numbers of any one or more of the following cells asthey are commonly understood to those persons skilled in the art:inflammatory monocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells,CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells.Optionally, the macrophages may include any one or more of thefollowing: M1-like macrophages or M2-like macrophages as those termshave been defined herein. Optionally, comparing the characteristic ofthe immune response may involve comparing a shift in an activation stateof macrophages. Further and optionally, the macrophages may shift frombeing M2-like macrophages to being M1-like macrophages. Optionally, themacrophages may shift from being M1-like macrophages to being M2-likemacrophages.

Further and optionally, comparing the characteristic of the immuneresponse may involve identifying, in the quantifiable and referenceimmune samples, cellular markers on any one or more of the followingcells as they are commonly understood to those persons skilled in theart: inflammatory monocytes, macrophages, CD11b+Gr-1+ cells, dendriticcells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NKcells. The macrophages may include any one or more of the following:M1-like macrophages or M2-like macrophages as those terms have beendefined herein. Optionally, comparing the characteristic of the immuneresponse may involve identifying, in the quantifiable and referenceimmune samples, cytokines produced by any one or more of the followingcells as they are commonly understood to those persons skilled in theart: inflammatory monocytes, macrophages, CD11b+Gr-1+ cells, dendriticcells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NKcells. Optionally, the macrophages may include any one or more of thefollowing: M1-like macrophages or M2-like macrophages. Further,cytokines may be produced as a result of a shift in an activation stateof the macrophages. The macrophages may shift from being M2-likemacrophages to being M1-like macrophages. Optionally, the macrophagesmay shift from being M1-like macrophages to being M2-like macrophages.

Further and optionally, comparing the characteristic of the immuneresponse may involve identifying, in the quantifiable and referenceimmune samples, differential gene expression produced by any one or moreof the following cells as they are commonly understood to those personsskilled in the art: inflammatory monocytes, macrophages, CD11b+Gr-1+cells, dendritic cells, CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ Tcells, or NK cells. The macrophages may include any one or more of thefollowing: M1-like macrophages or M2-like macrophages. Optionally, thedifferential gene expression may be produced as a result of a shift inan activation state of the macrophages. Further and optionally, themacrophages may shift from being M2-like macrophages to being M1-likemacrophages. The macrophages may shift from being M1-like macrophages tobeing M2-like macrophages.

In another aspect, a method of monitoring efficacy of a treatment regimein an individual being treated for a cancer in a specific organ ortissue is provided. The method involves measuring a characteristic of animmune response in a post-treatment immune sample obtained from thespecific organ or tissue after the individual has been subject to thetreatment regime for a period of time, wherein the presence of acharacteristic of the immune response which is greater in magnitude thanwould be expected had the individual not been subject to the treatmentregime, is indicative of the efficacy of the treatment regime; and thetreatment regime involves administering a preparation comprising one ormore antigenic determinants of a microbial pathogen which is pathogenicin the corresponding specific organ or tissue in a healthy subject.

The method detailed herein may further involve measuring thecharacteristic of the immune response in a pre-treatment referencesample, wherein the pre-treatment reference sample was obtained from thespecific organ or tissue before, at the same time as or aftercommencement of the treatment regime, but prior to obtaining thepost-treatment immune sample, and comparing the characteristic of theimmune response in the pre-treatment and post-treatment samples, whereinan increase in the magnitude of the immune response in thepost-treatment immune sample compared to the pre-treatment referencesample is indicative of the efficacy of the treatment regime.Optionally, measuring the characteristic of the immune response mayinvolve determining an indication of the number of inflammatorymonocytes in a sample of the organ or tissue. Optionally, measuring thecharacteristic of the immune response may involve determining anindication of the number of macrophages in a sample of the organ ortissue. The macrophages may include any one or more of the following:M1-like macrophages or M2-like macrophages.

Optionally, measuring the characteristic of the immune response mayinvolve determining an indication of the number of CD11 b+Gr-1+ cells ina sample of the organ or tissue or determining an indication of thenumber of dendritic cells in a sample of the organ or tissue. Furtherand optionally, measuring the characteristic of the immune response mayinvolve determining an indication of the number of CD11c+ MHC class II+cells in a sample of the organ or tissue or determining an indication ofthe number of CD4+ T cells in a sample of the organ or tissue ordetermining an indication of the number of CD8+ T cells in a sample ofthe organ or tissue.

Optionally, measuring the magnitude of the immune response may involvedetermining an indication of the number of NK cells in a sample of theorgan or tissue. Further and optionally, comparing the characteristic ofthe immune response may involve identifying, in the reference and immunesamples, cellular markers on any one or more of the following cells asthey are commonly understood to those persons skilled in the art:inflammatory monocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells,CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells.Optionally, the macrophages may include any one or more of thefollowing: M1-like macrophages or M2-like macrophages.

Further and optionally, comparing the characteristic of the immuneresponse may involve identifying, in the reference and immune samples,cytokines produced by any one or more of the following cells as they arecommonly understood to those persons skilled in the art: inflammatorymonocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells, CD11c+ MHCclass II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Themacrophages may include any one or more of the following: M1-likemacrophages or M2-like macrophages. Optionally, the cytokines may beproduced as a result of a shift in an activation state of themacrophages. The macrophages may shift from being M2-like macrophages tobeing M1-like macrophages. Further and optionally, the macrophages mayshift from being M1-like macrophages to being M2-like macrophages.

Optionally, comparing the characteristic of the immune response mayinvolve identifying, in the reference and immune samples, differentialgene expression produced by any one or more of the following cells asthey are commonly understood to those persons skilled in the art:inflammatory monocytes, macrophages, CD11b+Gr-1+ cells, dendritic cells,CD11c+ MHC class II+ cells, CD4+ T cells, CD8+ T cells, or NK cells. Themacrophages may include any one or more of the following: M1-likemacrophages or M2-like macrophages. The differential gene expression maybe produced as a result of a shift in an activation state of themacrophages. The macrophages may shift from being M2-like macrophages tobeing M1-like macrophages. Optionally, the macrophages may shift frombeing M1-like macrophages to being M2-like macrophages.

In various aspects, embodiments of the invention relate to a method oftreating a cancer situated in a lung in a subject. The method involvesadministering to the subject an effective amount of an antigen of one ormore microbial species that is pathogenic in the lung and administeringto the subject an effective amount of a platinum-containingchemotherapeutic agent. The microbial species may be a viral pathogen ora bacterial pathogen or a fungal pathogen.

As used herein, the phrase “treating a cancer” may include, withoutlimitation, reducing the lung tumour burden in a subject or increasinglife expectancy in a subject that has lung cancer. It will be understoodthat there are numerous biological read-outs that can be used by aperson skilled in the art to determine whether a cancer is being treatedor not.

The viral pathogen utilized herein may be, without limitation:influenza, adenovirus, respiratory syncytial virus, parainfluenza,monkeypox, herpes simplex virus (1 and 2), Varicella zoster,cytomegalovirus, Epstein-Barr virus, coronavirus, human metapneumovirus,Hendra virus, Nipah virus, Hantavirus, Lassa virus, human T-celllymphotrophic virus, cocksackievirus, echovirus, enterovirus, orrhinovirus, or any virus that is pathogenic in the lung.

The bacterial pathogen utilized herein may be, without limitation:Streptococcus pneumoniae, Moraxella catarrhalis, Mycoplasma pneumoniae,Klebsiella pneumoniae, Haemophilus influenza, Staphylococcus aureus,Chlamydia pneumoniae, Legionella pneumophila, or Bordatella pertussis orany bacterium that is pathogenic in the lung.

The fungal pathogen utilized herein may be, without limitation:Aspergillus fumigatus, Blastomyces sp., Coccidiodes immitis, Coccidiodesposadasii, Cryptococcus neoformans, Cryptococcus gattii, Fusarium sp.,Histoplasma capsulatum, Paecilomyces sp., Paracoccidioides brasiliensis,Penicillium mameffei, Pneumocystis jiroveci, Pseudallescheria boydi,Scedosporium apiospermum, Rhizopus sp., Mucor sp., Absidia sp.,Cunninghamella sp., Scedosporium prolificans, Stachybotrys chartarum,Trichoderma longibrachiatium, Trichosporon sp., or any fungus that ispathogenic in the lung.

As used herein, the term “platinum-containing chemotherapeutic agent”includes, but is not limited to: Cisplatin, carboaplatin or ormaplatin,oxaliplatin, DWA2114R ((−)-(R)-2aminomethylpyrrolidine (1,1-cyclobutanedicarboxylato) platinum), zeniplatin, enloplatin, lobaplatin, CI-973(SP-43(R)-I,I-cyclobutane-dicarboxylato(2-)-(2-methyl-1,4-65butanediamine-N,N′)platinum), 254-S nedaplatin, JM-216(bis-acetato-ammine-dichloro-cyclohexylamineplatinum(IV)), (see: Weiss,R. B. and Christian, M. C., “New Cisplatin Analogue in Development,”Drugs. 46:(03) 360-377 (1993)); CPA)2Pt[DOLYM] and (DACH)Pt[DOLYM]cisplatin (Choi et al., Arch. Pharmacol Res. 22(2):151-156, 1999); 254-Scisplatin analogue (Koga et al., Neurol. Res. 18(3):244-247, 1996);cis-1,4-diaminocyclohexane cisplatin analogues (Shamsuddin et al., J.Inorg. Biochem. 61(4): 291-301, 1996); MeOH cisplatin (Shamsuddin etal., Inorg. Chem. 36(25):59695971, 1997); CI-973 cisplatin analogue(Yang et al. Int. J. Oncol. 5(3):597-602, 1994);cis-diaminedichloroplatinum (II) and its analoguescis-I,I-cyclobutanedicarbosylato(2R)2-methyl-1,4-butanediamineplatinum(II)and cis-diammine (glycolato)platinum (Claycamp & Zimbrick, J. Inorg.Biochem. 26(4):257-67, 1986; Fan et al. Cancer Res. 48(11): 3135-9,1988; Heiger-Bemays et al. Biochemistry 29(36): 8461-6, 1990; Kikkawa etal., J. Exp. Clin. Cancer Res. 12(4):233-40, 1993; Murray et al.Biochemistry 31(47):11812-17, 1992; Takahashi et al., Cancer Chemother.Pharmacol. 33(1):31-5, 1993), gem-diphosphonate cisplatin analogues (FR2683529), cisplatin analogues containing a tethered dansyl group(Hartwig et al., J. Am. Chem. Soc. 114(21):8292-3, 1992),aminoalkylaminoanthraquinone-derived cisplatin analogues (Kitov et al.,Eur. J. Med. Chem. 23(4):381-3, 1988), spiroplatin, carboplatin,iproplatin and JM40 platinum analogues (Schroyen et al., Eur. J. CancerClin. Oncol. 24(8): 1309-12, 1988), and JM8 and JM9 cisplatin analogues(Harstrick et al., Int. J. Androl. 10(1); 139-45, 1987).

In another aspect, use of an effective amount of an antigen of one ormore microbial species that is pathogenic in the lung is provided toformulate a medicament for use with a platinum-containingchemotherapeutic agent for treating lung cancer in a subject. In anotheraspect, use of an effective amount of an antigen of one or moremicrobial species that is pathogenic in the lung is provided for usewith a platinum-containing chemotherapeutic agent, as detailed herein,for treating lung cancer in a subject. The microbial species may be aviral pathogen or a bacterial pathogen or a fungal pathogen, as detailedherein.

In another aspect, an effective amount of an antigen of one or moremicrobial species that is pathogenic in the lung is provided toformulate a medicament for use with a platinum-containingchemotherapeutic agent for treating lung cancer in a subject. In anotheraspect, an effective amount of an antigen of one or more microbialspecies that is pathogenic in the lung is provided for use with aplatinum-containing chemotherapeutic agent, as detailed herein, fortreating lung cancer in a subject. The microbial species may be a viralpathogen or a bacterial pathogen or a fungal pathogen, as detailedherein. The platinum-containing chemotherapeutic agent may be, withoutlimitation: Cisplatin, carboplatin or oxaliplatin.

In another aspect, a kit is provided. The kit includes an antigen of oneor more microbial species that is pathogenic in the lung, aplatinum-containing chemotherapeutic agent; and instructions forproviding the antigen and the platinum-containing chemotherapeutic agentto a subject in need thereof. The microbial species may be a viralpathogen or a bacterial pathogen or a fungal pathogen, as detailedherein.

In various aspects, embodiments of the invention relate to compositionscomprising components of organisms that may cause infections of thegastrointestinal tract, so that the organism may be characterized as apathogen. However, an organism that is in some cases pathogenic may notalways cause disease. Most animals are colonized to some degree by otherorganisms, such as bacteria, which generally exist in symbiotic orcommensal relationships with the host animal. Thus, many species ofnormally harmless bacteria are found in healthy animals, and are usuallylocalized to the surface of specific organs and tissues. Often, thesebacteria aid in the normal functioning of the body. For example, inhumans, symbiotic Escherichia coli bacteria may be found in theintestine, where they promote immunity and reduce the risk of infectionwith more virulent pathogens.

Bacteria that are generally harmless, such as Escherichia coli, cancause infection in healthy subjects, with results ranging from mild tosevere infection to death. Whether or not an organism, such as abacterium, is pathogenic (i.e., causes infection) depends to some extenton factors such as the route of entry and access to specific host cells,tissues, or organs; the intrinsic virulence of the bacterium; the amountof the bacteria present at the site of potential infection; or thehealth of the host animal. Thus, organisms that are normally harmlesscan become pathogenic given favorable conditions for infection, and evenvirulent organisms may require specific circumstances to causeinfection. Accordingly, organisms that are members of the normal floracan be pathogens when they move beyond their normal ecological role inthe endogenous flora. For example, endogenous species can causeinfection outside of their ecological niche in regions of anatomicalproximity, for example by contiguous spread. When this occurs, and inthe context of the present invention, these normally harmless endogenousorganisms are considered pathogenic.

Specific organisms, such as bacterial species, viruses, worms, andprotozoa are known to cause infections in specific regions of the GIT inotherwise healthy subjects. Examples of organisms that commonly causeinfections in specific regions of the GIT are listed below; it will beunderstood that these examples are not intended to be limiting and thata skilled person would be able to readily recognize and identifyinfectious or pathogenic organisms that cause infections, or commonlycause infections, in various regions of the GIT in healthy adults, basedfor example on knowledge about particular patient populations, asrepresented for example by the following publications: Manual ofClinical Microbiology 8th Edition, Patrick Murray, Ed., 2003, ASM PressAmerican Society for Microbiology, Washington D.C., USA; Mandell,Douglas, and Bennett's Principles and Practice of Infectious Diseases5th Edition, G. L. Mandell, J. E. Bennett, R. Dolin, Eds., 2000,Churchill Livingstone, Philadelphia, Pa., USA, all of which areincorporated by reference herein.

Infections of the mouth are commonly caused by the following bacterialspecies: Prevotella melaninogenicus, anaerobic streptococci, viridansstreptococci, Actinomyces spp., Peptostreptococcus spp., or Bacteroidesspp., or other oral anaerobes; or viral pathogens: herpes simplex,coxsackieviruses, or Epstein-Barr.

Infections of the esophagus are commonly caused by the followingbacterial species: Actinomyces spp., Mycobacterium avium, Mycobacteriumtuberculosis, or Streptococcus spp.; or viral pathogens:cytomegalovirus, herpes simplex, or varicella-zoster.

Infections of the stomach are commonly caused by the following bacterialspecies: Streptococcus pyogenes or Helicobacter pylori; or viralpathogens: cytomegalovirus, herpes simplex, Epstein-Barr, rotaviruses,noroviruses, or adenoviruses.

Infections of the small bowel are commonly caused by the followingbacterial species: Escherichia coli, Clostridium difficile, Bacteroidesfragilis, Bacteroides vulgatus, Bacteroides thetaiotaomicron,Clostridium perfringens, Salmonella enteriditis, Yersiniaenterocolitica, or Shigella flexneri; or viral pathogens: adenoviruses,astroviruses, caliciviruses, noroviruses, rotaviruses, orcytomegalovirus.

Infections of the colon/rectum are commonly caused by the followingbacterial species: Escherichia coli, Clostridium difficile, Bacteroidesfragilis, Bacteroides vulgatus, Bacteroides thetaiotaomicron,Clostridium perfringens, Salmonella enteriditis, Yersiniaenterocolitica, or Shigella flexneri; or viral pathogens: adenoviruses,astroviruses, caliciviruses, noroviruses, rotaviruses, orcytomegalovirus.

Infections of the anus are commonly caused by the following bacterialspecies: Streptococcus pyogenes, Bacteroides spp., Fusobacterium spp.,anaerobic streptococci, Clostridium spp., Escherichia coli, Enterobacterspp., Pseudomonas aeruginosa, or Treponema pallidum; or viral pathogens:herpes simplex.

Organisms such as bacteria are often classified operationally ascollections of similar strains (which generally refer to groups ofpresumed common ancestry with identifiable physiological but usually notmorphological distinctions, and which may be identified usingserological techniques against bacterial surface antigens). Thus, eachbacterial species (e.g., Escherichia coli) has numerous strains (orserotypes), which may differ in their ability to cause infection ordiffer in their ability to cause infection in a particular organ/site.Certain strains of Escherichia coli are more likely to causegastrointestinal infection/diarrhea, including enterotoxigenic E. coli(ETEC), enteropathogenic E. coli (EPEC), enterohemorrhagic E. coli(EHEC), Shiga toxin-producing E. coli (STEC), enteroaggregative E. coli(EAEC), enteroinvasive E. coli (EIEC) and diffuse adhering E. coli(DAEC). In accordance with the present invention, one or more of anETEC, EPEC, EHEC, STEC, EAEC, EIEC or DAEC strains of E. coli (i.e.,strains that cause colon infection), may be chosen for a formulation totreat and IBD.

Similarly, there may be numerous subtypes of specific viruses, worms, orprotozoa, which are associated with disease in a particular population,and are therefore amenable for use in the present invention.

The compositions of the invention include antigens of organisms that arepathogenic in a specific region of the GIT. The compositions may includethe components of whole organisms, whole cells or whole virions, or mayinclude extracts or preparations of the organisms, such as cell wall orcell membrane extracts, or exotoxins. The compositions may also includeone or more isolated antigens from these organisms. Pathogenic organismsmay be available commercially (for example from the American TypeCulture Collection, Manassas, Va., USA), or may be clinical isolatesfrom subjects having an infection.

The compositions of the invention derived from pathogens can be providedalone or in combination with other compounds (for example, nucleic acidmolecules, small molecules, peptides, or peptide analogues), in thepresence of a liposome, an adjuvant, or any pharmaceutically acceptablecarrier, in a form suitable for administration to mammals, for example,humans. As used herein “pharmaceutically acceptable carrier” or“excipient” includes any and all solvents, dispersion media, coatings,antibacterial and antifungal agents, isotonic and absorption delayingagents, and the like that are physiologically compatible. The carriercan be suitable for any appropriate form of administration, includingsubcutaneous, intradermal, intravenous, parenteral, intraperitoneal,intramuscular, sublingual, inhalational, intratumoral or oraladministration. Pharmaceutically acceptable carriers include sterileaqueous solutions or dispersions and sterile powders for theextemporaneous preparation of sterile injectable solutions ordispersion. The use of such media and agents for pharmaceutically activesubstances is well known in the art. Except insofar as any conventionalmedia or agent is incompatible with the active compound (i.e., thespecific bacteria, bacterial antigens, or compositions thereof of theinvention), use thereof in the pharmaceutical compositions of theinvention is contemplated. Supplementary active compounds can also beincorporated into the compositions.

Methods well known in the art for making formulations are found in, forexample, “Remington's Pharmaceutical Sciences” (20th edition), ed. A.Gennaro, 2000, Mack Publishing Company, Easton, Pa. Formulations forparenteral administration may, for example, contain excipients, sterilewater, or saline, polyalkylene glycols such as polyethylene glycol, oilsof vegetable origin, or hydrogenated napthalenes. Biocompatible,biodegradable lactide polymer, lactide/glycolide copolymer, orpolyoxyethylene-polyoxypropylene copolymers may be used to control therelease of the compounds. Other potentially useful parenteral deliverysystems for include ethylene-vinyl acetate copolymer particles, osmoticpumps, implantable infusion systems, and liposomes. Formulations forinhalation may contain excipients, for example, lactose, or may beaqueous solutions containing, for example, polyoxyethylene-9-laurylether, glycocholate and deoxycholate, or may be oily solutions foradministration in the form of nasal drops, or as a gel. For therapeuticor prophylactic compositions, the formulations may be administered to anindividual in an amount effective to stop or slow progression of theIBD.

An “effective amount” of a pathogenic species or antigen thereofaccording to the invention includes a therapeutically effective amountor a prophylactically effective amount. A “therapeutically effectiveamount” refers to an amount effective, at dosages and for periods oftime necessary, to achieve the desired therapeutic result, such asreduction or elimination of symptoms of IBD. A therapeutically effectiveamount of a pathogenic species or antigen(s) thereof may vary accordingto factors such as the disease state, age, sex, and weight of theindividual, and the ability of the compound to elicit a desired responsein the individual. Dosage regimens may be adjusted to provide theoptimum therapeutic response. A therapeutically effective amount mayalso be one in which any toxic or detrimental effects of the pathogenicspecies or antigen thereof are outweighed by the therapeuticallybeneficial effects. A “prophylactically effective amount” refers to anamount effective, at dosages and for periods of time necessary, toachieve the desired prophylactic result, such as prevention of IBD.Typically, a prophylactic dose is used in subjects prior to or at anearlier stage of IBD, so that a prophylactically effective amount may beless than a therapeutically effective amount.

For administration by subcutaneous or intradermal injection, anexemplary range for therapeutically or prophylactically effectiveamounts of one or more pathogenic bacterial species may be about 1million to 100,000 million organisms per ml, or may be 100 million to7000 million organisms per ml, or may be 500 million to 6000 millionorganisms per ml, or may be 1000 million to 5000 million organisms perml, or may be 2000 million to 4000 million organisms per ml, or anyinteger within these ranges. The total concentration of bacteria per mlmay range from 1 million to 100,000 million organisms per ml, or may be50 million to 7000 million organisms per ml, or may be 100 million to6000 million organisms per ml, or may be 500 million to 5000 millionorganisms per ml, or may be 1000 million to 4000 million organisms perml, or any integer within these ranges. The range for therapeutically orprophylactically effective amounts of antigens of a pathogenic bacterialspecies may be any integer from 0.1 nM-0.1 M, 0.1 nM-0.05M, 0.05 nM-15μM or 0.01 nM-10 μM.

It is to be noted that dosage concentrations and ranges may vary withthe severity of the condition to be alleviated, or may vary with thesubject's immune response. In general, the goal is to achieve anadequate immune response. For administration by subcutaneous orintradermal infection, the extent of an immune response may bedetermined, for example, by size of delayed local immune skin reactionat the site of injection (e.g., from 0.25 inch to 4 inch diameter). Thedose required to achieve an appropriate immune response may varydepending on the individual (and their immune system) and the responsedesired. Standardized dosages may also be used.

In the context of subcutaneous or intradermal administration, if thegoal is to achieve a 2 inch local skin reaction, using a bacterialcomposition, the total dose may, for example, range from 2 millionbacteria (e.g., 0.001 ml of a vaccine with a concentration of 2,000million organisms per ml) to more than 20,000 million bacteria (e.g., 1ml of a vaccine with a concentration of 20,000 million organisms perml). The concentrations of individual bacterial species or antigensthereof within a composition may also be considered. For example, if theconcentration of one particular pathogenic bacterial species, cell sizeof that species or antigenic load thereof is much higher relative to theother pathogenic bacterial species in the vaccine, then the local immuneskin reaction of an individual may be likely due to its response to thisspecific bacterial species. In some embodiments, the immune system of anindividual may respond more strongly to one bacterial species within acomposition than another, depending for example on past history ofexposure to infection by a particular species, so the dosage orcomposition may be adjusted accordingly for that individual.

For any particular subject, the timing and dose of treatments may beadjusted over time (e.g., timing may be daily, every other day, weekly,monthly) according to the individual need and the professional judgementof the person administering or supervising the administration of thecompositions. For example, in the context of subcutaneous or intradermaladministration, the compositions may be administered every second day.An initial dose of approximately 0.05 ml may be administeredsubcutaneously, followed by increases from 0.01-0.02 ml every second dayuntil an adequate skin reaction is achieved at the injection site (forexample, a 1 inch to 2 inch diameter delayed reaction of visible rednessat the injection site). Once this adequate immune reaction is achieved,this dosing is continued as a maintenance dose. The maintenance dose maybe adjusted from time to time to achieve the desired visible skinreaction (inflammation) at the injection site. Dosing may be for adosage duration, for example of at least 2 weeks, 2 months, 6 months, 1,2, 3, 4, or 5 years or longer.

In some embodiments, the invention may include antigenic compositionsadministered to one or more epithelial tissues by a non-enteric route.For example: to skin by intradermal or subcutaneous injection; to lungepithelium by inhalation. Accordingly, in some embodiments the antigeniccompositions of the invention are administered so as to provoke animmune response in a non-enteric tissue, such as an epithelial tissue.In some embodiments, one or more non-enteric routes of administrationmay be combined with one or more additional routes of administration,such as intratumoral, intramuscular or intravenous administration.

In various aspects of the invention, the antigenic compositions that areadministered to a patient may be characterized as having an antigenicsignature, i.e., a combination of antigens or epitopes that issufficiently specific that the antigenic composition is capable ofeliciting an immune response that is specific to a particular pathogen,such as an adaptive immune response.

The amount of active compound (e.g., bacterial species, viruses,protozoa or helminths, or antigens thereof) in compositions of theinvention may vary according to factors such as the disease state, age,sex, and weight of the individual. Dosage regimens may be adjusted toprovide the optimum therapeutic response. For example, a single bolusmay be administered, several divided doses may be administered over timeor the dose may be proportionally reduced or increased as indicated bythe exigencies of the therapeutic situation. It may be advantageous toformulate parenteral compositions in dosage unit form for ease ofadministration and uniformity of dosage.

In the case of antigenic formulations (analogous to a vaccine), animmunogenically effective amount of a compound of the invention can beprovided, alone or in combination with other compounds, with animmunological adjuvant. The compound may also be linked with a carriermolecule, such as bovine serum albumin or keyhole limpet hemocyanin toenhance immunogenicity. An antigenic composition (“vaccine”) is acomposition that includes materials that elicit a desired immuneresponse. An antigenic composition may select, activate or expand memoryB, T cells, neutrophils, monocytes or macrophages of the immune systemto, for example, reduce or eliminate the symptoms of the IBD. In someembodiments, the specific pathogenic microbe, virus, viral antigens,bacteria, bacterial antigens, or compositions thereof of the inventionare capable of eliciting the desired immune response in the absence ofany other agent, and may therefore be considered to be an antigeniccomposition. In some embodiments, an antigenic composition includes asuitable carrier, such as an adjuvant, which is an agent that acts in anon-specific manner to increase the immune response to a specificantigen, or to a group of antigens, enabling the reduction of thequantity of antigen in any given vaccine dose, or the reduction of thefrequency of dosage required to generate the desired immune response. Abacterial antigenic composition may include live or dead bacteriacapable of inducing an immune response against antigenic determinantsnormally associated with the bacteria. In some embodiments, an antigeniccomposition may include live bacteria that are of less virulent strains(attenuated), and therefore cause a less severe infection. In someembodiments the antigenic composition may include live, attenuated ordead viruses capable of inducing an immune response against antigenicdeterminants normally associated with the virus.

An antigenic composition comprising killed organisms for administrationby injection may be made as follows. The organism may be grown insuitable media, and washed with physiological salt solution. Theorganism may then be centrifuged, resuspended in saline solution, andkilled with heat. The suspensions may be standardized by directmicroscopic count, mixed in required amounts, and stored in appropriatecontainers, which may be tested for safety, shelf life, and sterility inan approved manner. In addition to the organism and/or antigens thereof,a killed preparation suitable for administration to humans may includephenol preservative (for example 0.4%) and/or sodium chloride (forexample on the order of 0.9%). The composition may also for exampleinclude trace amounts of brain heart infusion (beef), peptones, yeastextract, agar, sheep blood, dextrose, sodium phosphate and/or othermedia components.

In some embodiments, the antigenic composition may be used as an aerosolfor inhalation.

In general, the compositions of the invention should be used withoutcausing substantial toxicity. Toxicity of the compounds of the inventioncan be determined using standard techniques, for example, by testing incell cultures or experimental animals and determining the therapeuticindex, i.e., the ratio between the LD50 (the dose lethal to 50% of thepopulation) and the LD100 (the dose lethal to 100% of the population).

In some embodiments, bacteria that are members of the endogenous floraof a particular region of the GIT may be used to formulate antigeniccompositions of the invention. The rows of Table 1 list a number ofbacterial species, together with the biological regions in which eachspecies may form a part of the endogenous flora. For example,Abiotrophia spp. are typically members of the endogenous flora of themouth.

TABLE 1 Human Bacterial Normal Flora (Endogenous Bacterial HumanPathogens) Duodenum/ Bacterial species Mouth Stomach Jejunum Ileum ColonCFU/mL 10{circumflex over ( )}5 10{circumflex over ( )}2 10{circumflexover ( )}5 10{circumflex over ( )}8 10{circumflex over ( )}11Abiotrophia spp + Acholeplasma + laidlawii Acidaminococcus + + + +fermentans Acinetobacter + + + + spp. Actinobacillus + spp.Actinobaculum + + + + spp. Actinomyces + + + + spp. Aeromonas spp. + + +Anaerorhabdus + + furcosus Anaerococcus + + hydrogenalisAnaerococcus + + lactolyticus Anaerococcus + + prevotii Atopobiumspp. + + + + Bacillus spp. + + Bacteroides + + caccae Bacteroides + +distasonis Bacteroides + + eggerthii Bacteroides + + fragilisBacteroides + + merdae Bacteroides + + ovatus Bacteroides + +splanchnicus Bacteroides + + thetaiotaomicron Bacteroides + + vulgatusBifidobacterium + + + adolescentis Bifidobacterium + + + bifidumBifidobacterium + + + breve Bifidobacterium + + + catenulatumBifidobacterium + + + + dentium Bifidobacterium + + + longumBilophila + + + + wadsworthia Burkholderia + + + cepaciaButyrivibrio + + + fibrisolvens Campylobacter + + + concisusCampylobacter + + + curvus Campylobacter + + + gracilisCampylobacter + + + jejuni Campylobacter + + + rectusCampylobacter + + + + showae Campylobacter + sputorum Capnocytophaga +granulosum Capnocytophaga + gingivalis Campylobacter + haemolyticaCapnocytophaga + + + + ochracea Capnocytophaga + sputigenaCardiobacterium + hominis Cedecea spp + Centipeda + periodontiiCitrobacter + + + freundii Citrobacter + + + koseri Clostridiumspp. + + + Corynebacterium + accolens Corynebacterium + afermentansDesulfomonas + + + pigra Dysgonomonas + + + spp. Eikenella + + + +corrodens Enterobacter + + + aerogenes Enterobacter + + + cloacaeEnterobacter + + + gergoviae Enterobacter + + + sakazakiiEnterobacter + + + taylorae Enterococcus + + + spp. Escherichiacoli + + + Escherichia + + + fergusonii Escherichia + + + hermanniiEscherichia + + + vulneris Eubacterium spp. + + + + Ewingella +americana Finegoldia + + + magnus Fusobacterium + alocisFusobacterium + + + gonidiaformans Fusobacterium + + + mortiferumFusobacterium + + + naviforme Fusobacterium + + + + necrophorumFusobacterium + + nucleatum Fusobacterium + sulci Fusobacterium + + +russii Fusobacterium + + + varium Gardnerella + + + vaginalis Gemella +haemolysans Gemella + + + + morbillorum Globicatella spp. + +Granulicatella + spp. Haemophilus + spp. Hafnia alvei + + + Helcococcuskunzii Helicobacter spp. + + + Kingella spp. + Klebsiella spp. + + + +Lactobacillus + + + + + acidophilus Lactobacillus + breveLactobacillus + casei Lactobacillus + + + + + fermentumLactobacillus + + + + reuteri Lactobacillus + + + + + salivariusLeclercia + + + adecarboxylata Leminorella spp. + + + Leptotrichia +buccalis Megasphaera + + + elsdenii Micrococcus + luteus Micrococcus +lylae Micromonas + micros Mitsuokella + + + multiacidus Mobiluncus + + +curisii Mobiluncus + + + mulieris Moellerella + + + wisconsensisMoraxella + catarrhalis other Moraxella + spp. Morganella + + + morganiiMycoplasma + buccale Mycoplasma + fermentans Mycoplasma + hominisMycoplasma + lipophilum Mycoplasma + orale Mycoplasma + pneumoniaeMycoplasma + salivarium Pantoea + + + agglomerans Pasteurella +multocida Pediococcus + + spp. Peptoniphilus + + + asaccharolyticusPeptostreptococcus + + + + anaerobus Peptostreptococcus + + + productusPorphyromonas + + + + asaccharolytica Porphyromonas + + catoniaePorphyromonas + + endodontalis Porphyromonas + + gingivalisPrevotella + + buccae Prevotella + + buccalis Prevotella + + corporisPrevotella + + dentalis Prevotella + + denticola Prevotella + + enoecaPrevotella + + heparinolytica Prevotella + + intermedia Prevotella + +loescheii Prevotella + + melaninogenica Prevotella + + nigrescensPrevotella oralis + + Prevotella oris + + Prevotella + + oulorumPrevotella + + tannerae Prevotella + + veroralis Prevotella + +zoogleoformans Propionibacterium + propionicum Proteus mirabilis + +Proteus penneri + + Proteus vulgaris + + Providencia + + rettgeriProvidencia + + + stuartii Pseudomonas + + + aeruginosaRetortamonas + + + intestinalis Rothia + dentocariosa Rothia +mucilaginosa Ruminococcus + + + productus Selenomonas + spp.Serratia + + liquefaciens Serratia + + marcescens Serratia odorifera + +Staphylococcus + aureus Staphylococcus + epidermidis Streptococcus + + +agalactiae Streptococcus + + + + anginosus Streptococcus + + + bovisStreptococcus + + + + constellatus Streptococcus + cricetiStreptococcus + crista Streptococcus + equisimilis Streptococcus +gordonii Streptococcus + + + intermedius Streptococcus + + mitisStreptococcus + mutans Streptococcus + oralis Streptococcus +parasanguis Streptococcus + + pyogenes Streptococcus + + salivariusStreptococcus + + sanguis Streptococcus + sobrinus Streptococcus +vestibularis Group C + G + + Streptococci Succinivibrio + + +dextrinosolvens Sutterella spp. + + + Suttonella + indologenesTissierella + + + praeacuta Treponema + denticola Treponema +maltophilum Treponema + socranskii Treponema + vincentii Ureaplasma +urealyticum Veillonella spp. + + + +

Endogenous microbial flora, such as bacteria, have access to tissues forpathogenesis either through contiguous spread or bacteremic spread.Under favorable conditions, all endogenous organisms can becomepathogenic and invade locally and spread by contiguous spread toadjacent tissues and organs. Endogenous bacterial flora of the skin,mouth and colon are the species that are understood to also be amenableto bacteremic spread. Bacteria that are members of a particularendogenous flora domain may therefore cause infection in tissues ororgans to which these bacteria may spread. Accordingly, one aspect ofthe invention involves the use of endogenous microbial pathogens totreat an IBD having symptoms localized to a region of the GIT in whichthe endogenous bacteria may spread to cause infection. The columns ofTable 2 list domains for endogenous flora. The rows of Table 2 listregions of the GIT within which IBD may be situated. Accordingly, oneaspect of the invention involves the use of endogenous microbialpathogens to formulate antigenic compositions, or the selection ofexisting formulations having the pathogens, for treating an IBD situatedin the region of the GIT to which the pathogen may spread to cause aninfection. Accordingly, in alternative embodiments, an IBD that issymptomatic in the region listed in the first column of Table 2 may betreated with antigenic compositions comprising antigenic determinantsthat are specific for microbial pathogens that are members of theendogenous flora of one or more of the endogenous flora domains listedin the first row of Table 2 and indicated with an X or a check mark inthe appropriate row.

TABLE 2 Tissue/Organ Pathogenicity of Endogenous Flora Tissue/organDuo-denum/ site Mouth Stomach Jejunum Ileum Colon Oral x Tonsil xNasopharynx/ x Sinus Esophagus x Stomach x Small bowel x x Colon/Rectumx Anus x

In accordance with the combined information in Tables 1 and 2, IBDmanifest in a particular region of the GIT set out in column 1 of Table2 may be treated with antigenic compositions comprising antigenicdeterminants of the corresponding bacterial species of Table 1, so thatthe column headings in Table 2 are in effect replaced with the bacterialspecies of Table 1.

In some embodiments, pathogens for use in the invention may be exogenousbacterial pathogens. For example, the organisms listed in Table 3 may beused as microbial pathogens to formulate antigenic compositions, orantigenic compositions having those pathogens may selected, for use totreat an IBD situated in the region of the GIT listed with the relevantorganism in Table 3. In some embodiments, antigenic determinants of bothendogenous and exogenous bacterial species targeted to a specific tissueor organ may be used in combination. For example, an antigeniccomposition derived from, or specific for, Clostridium difficile, may beused to treat a IBD situated in the colon.

TABLE 3 Exogenous Bacterial Human Pathogens, and their Sites ofInfection in the GIT Bacterial Species Region of the GIT Aerobacter spp.small bowel, colon, Bacillus anthracis oral, small bowel, colon,hematological Bacillus cereus colon, other Bacillus spp. colon, stomach,small bowel Brucella spp. small bowel, colon Campylobacter coli smallbowel, colon Campylobacter colon jejuni Campylobacter small bowel, colonsputorum Clostridium small bowel, colon, stomach bifermentansClostridium colon, small bowel botulinum Clostridium difficile colonClostridium indolis small bowel, colon, stomach, Clostridium smallbowel, colon, stomach mangenolii Clostridium small bowel, colon, stomachperfringens Clostridium sordellii small bowel, colon, stomachClostridium small bowel, colon, stomach sporogenes Clostridium smallbowel, colon, stomach subterminale Edwarsiella tarda small bowel, colonFrancisella small bowel tularensis Helicobacter pylori stomachLeptospirosis spp. oral Listeria small bowel, colon monocytogenesMycobacterium colon, small bowel bovis Mycobacterium small bowel, colontuberculosis Pediococcus spp. colon Plesiomonas small bowel, colonshigelloides Rickettsia small bowel rickettsiae Salmonella spp. stomach,small bowel, colon Shigella boydii colon Shigella colon dysenteriaeShigella flexneri colon Shigella sonnei colon other Spirillum spp. colonStreptococcus small bowel zooepidemicus Treponema oral, anus pallidumTropheryma small bowel, colon whipplei Vibrio cholerae colon, smallbowel Vibrio fluvialis small bowel, colon Vibrio furnissii small bowel,colon Vibrio hollisae small bowel, colon Vibrio colon, small bowelparahaemolyticus Yersinia small bowel, colon enterocolitica Yersiniasmall bowel, colon pseudotuberculosis

In some embodiments, pathogens for use in the invention may be viralpathogens. Table 4 provides an exemplary list of viral pathogenstogether with the tissue and organ sites for which each viral species isreportedly a pathogen. Accordingly, one aspect of the invention involvesutilizing immunogenic compositions that are specific for the namedviruses to treat an IBD situated in the region of the GIT that isidentified adjacent to the name of the virus in Table 4.

TABLE 4 Viral Human Pathogens and Their Sites of Infection Virus Regionof the GIT Herpes Simplex rectum, anus virus (1 and 2) Cytomegalovirussmall bowel, colon/rectum Epstein-Barr virus oral Adenovirus oral, smallbowel, colon Human papillomavirus anus, oral Orthoreoviruses smallbowel, colon, oral Coltiviruses oral Rotaviruses small bowel, colonAlphaviruses small bowel, colon, Coronaviruses oral, small bowel, colonToroviruses small bowel, colon Parainfluenza viruses oral Respiratorysyncytial virus oral Human metapneumovirus oral, small bowel, colonVesicular stomatitis virus oral, small bowel, colon Rabies virus oralInfluenza virus oral Hantaviruses oral Machupo virus small bowel, colonJunin virus small bowel, colon Poliovirus small bowel, colonCoxsackieviruses small bowel, colon Echoviruses oral, small bowel, colonHepatitis A virus small bowel, colon Rhinoviruses oral Noroviruses andother small bowel, colon Caliciviruses Astroviruses small bowel, colonPicobirnaviruses small bowel, colon Hepatitis E virus small bowel, colon

The cumulative information in Tables 1 through 4 provides an extensiveidentification of pathogens that may be used in the formulation ofantigenic compositions of the invention, together with an identificationof the region of the GIT in which these organisms are pathogenic, andaccordingly identifies the region of the GIT in which an IBD is situatedthat may be treated with an antigenic formulation of the invention.Pathogens may be selected from endogenous pathogens or exogenouspathogens.

In some embodiments, the pathogen selected for use in antigeniccompositions of the invention may be one that is a common cause of acuteinfection in the region of the GIT in which the IBD to be treated issituated. Table 5 identifies bacterial and viral pathogens of this kind,together with the region of the GIT in which they commonly causeinfection. Accordingly, in selected embodiments, an IBD residing in aregion of the GIT identified in the first column of Table 5 may betreated with an antigenic composition that comprises antigenicdeterminants for one or more of the pathogenic organisms listed in thesecond column of Table 5.

TABLE 5 Common causes of acute infection (bacteria and viruses) forselected regions of the GIT Selected regions of the GIT Common Bacterialor Viral Pathogens Oral Prevotella melaninogenicus, anaerobicstreptococci, viridans streptococci, Actinomyces spp.,Peptostreptococcus spp., Bacteroides spp., and other oral anaerobesherpes simplex, coxsackieviruses, Epstein-Barr Stomach Streptococcuspyogenes, Helicobacter pylori cytomegalovirus, herpes simplex,Epstein-Barr, rotaviruses, noroviruses, adenoviruses Small bowelEscherichia coli, Clostridium difficile, Bacteroides fragilis,Bacteroides vulgatus, Bacteroides thetaiotaomicron, Clostridiumperfringens, Salmonella enteriditis, Yersinia enterocolitica, Shigellaflexneri adenoviruses, astroviruses, caliciviruses, noroviruses,rotaviruses, cytomegalovirus Colon/ Escherichia coli, Clostridiumdifficile, Bacteroides fragilis, Rectum Bacteroides vulgatus,Bacteroides thetaiotaomicron, Clostridium perfringens, Salmonellaenteriditis, Yersinia enterocolitica, Shigella flexneri adenoviruses,astroviruses, caliciviruses, noroviruses, rotaviruses, cytomegalovirusAnus Streptococcus pyogenes, Bacteroides spp., Fusobacterium spp.,anaerobic streptococci, Clostridium spp., E. coli, Enterobacter spp.,Pseudomonas aeruginosa, Treponema pallidum herpes simplex

The specific organisms which commonly cause infection in a specificregion of the GIT may vary by geographical location. Table 5 is thus notan exhaustive list of common pathogens for all geographic locations andpopulation groups. It is understood that a clinical microbiologistskilled in the art could determine the common pathogenic species in aparticular geographic area or population group for a specific region ofthe GIT in accordance with the invention.

Humans are hosts to a wide range of gastrointestinal parasites,including various protozoa and helminths, which for purposes of thepresent invention constitute pathogens of the GIT (Schafer, T. W.,Skopic, A. Parasites of the small intestine. Curr Gastroenterol Reports2006; 8:312-20; Jernigan, J., Guerrant, R. L., Pearson, R. D. Parasiticinfections of the small intestine. Gut 1994; 35:289-93; Sleisenger &Fordtran's Gastrointestinal and liver disease. 8th ed. 2006; Garcia, L.S. Diagnostic medical parasitology. 5th ed. 2007). Compositions of theinvention may accordingly include antigenic components of variousprotozoa, including for example: Giardia lamblia, Cryptosporidiumparvum, Cryptosporidium hominus, Isospora belli, Sarcocystis species,Coccidian like bodies (Cyclospora species), Enterocytozoon bieneusi,Entamoeba histolytica, Entamoeba dispar, Entamoeba coli, Entamoebahartmanni, Endolimax nana, lodamoeba bütschlii, Dientameoba fragilis,Blastocystis hominus, Cyclospora cayetanensis, Microsporidia,Trypanosoma cruzi, Chilomastix mesnili, Pentatrichomonas hominis,Balantidium coli. Similarly, compositions of the invention may includeantigenic components of various helminths, including for example:Cestodes (tapeworms), Taenia saginata, Taenia solium, Diphyllobothriumspecies, Hymenolepis nana, Hymenolepis diminuta, Dipylidium caninum,Nematodes (round worms), Ascaris lumbricoides, Strongyloidesstercoralis, Necator americanus, Ancylostoma duodenale, Ancylostomacaninum, Tichuris trichiura, Capillaria philippinensis, Trichostrongylusspecies, Trichinella species, Necator americanus, Anisakis and relatedspecies, Angiostrongylus costaricensis, Enterobius vermicularis,Trematodes (flukes), Fasciolopsis buski, Heterophyes speicies,Echinostoma species, Clonorchis sinensis, Opisthorchis species, Fasciolaspecies, Metagonimus yokogawi, Schistosoma mansoni, Schistosomajaponicum, Schistosoma mekongi, Schistosoma intercalatum, Echinostomaspecies and Paragonimus species.

In accordance with the foregoing, in various aspects, the invention mayinvolve the treatment of an IBD with formulations of a pathogen isselected from the group consisting of: Acidaminococcus fermentans;Acinetobacter spp.; Actinobaculum spp.; Actinomyces spp.; Aeromonasspp.; Anaerorhabdus furcosus; Anaerococcus hydrogenalis; Anaerococcuslactolyticus; Anaerococcus prevotii; Atopobium spp.; Bacillus spp.;Bacteroides caccae; Bacteroides distasonis; Bacteroides eggerthii;Bacteroides fragilis; Bacteroides merdae; Bacteroides ovatus;Bacteroides splanchnicus; Bacteroides thetaiotaomicron; Bacteroidesvulgatus; Bifidobacterium adolescentis; Bifidobacterium bifidum;Bifidobacterium breve; Bifidobacterium catenulatum; Bifidobacteriumdentium; Bifidobacterium longum; Bilophila wadsworthia; Burkholderiacepacia; Butyrivibrio fibrisolvens; Campylobacter concisus;Campylobacter curvus; Campylobacter gracilis; Campylobacter jejuni;Campylobacter rectus; Campylobacter showae; Capnocytophaga ochracea;Cedecea spp; Citrobacter freundii; Citrobacter koseri; Clostridium spp.;Desulfomonas pigra; Dysgonomonas spp.; Eikenella corrodens; Enterobacteraerogenes; Enterobacter cloacae; Enterobacter gergoviae; Enterobactersakazakii; Enterobacter taylorae; Enterococcus spp.; Escherichia coli;Escherichia fergusonii; Escherichia hermannii; Escherichia vulneris;Eubacterium spp.; Finegoldia magnus; Fusobacterium gonidiaformans;Fusobacterium mortiferum; Fusobacterium naviforme; Fusobacteriumnecrophorum; Fusobacterium nucleatum; Fusobacterium russii;Fusobacterium varium; Gardnerella vaginalis; Gemella morbillorum;Globicatella spp.; Hafnia alvei; Helicobacter spp.; Klebsiella spp.;Lactobacillus acidophilus; Lactobacillus fermentum; Lactobacillusreuteri; Lactobacillus salivarius; Leclercia adecarboxylata; Leminorellaspp.; Megasphaera elsdenii; Mitsuokella multiacidus; Mobiluncus curisii;Mobiluncus mulieris; Moellerella wisconsensis; Morganella morganii;Pantoea agglomerans; Pediococcus spp.; Peptoniphilus asaccharolyticus;Peptostreptococcus anaerobus; Peptostreptococcus productus;Porphyromonas asaccharolytica; Proteus mirabilis; Proteus penneri;Proteus vulgaris; Providencia rettgeri; Providencia stuartii;Pseudomonas aeruginosa; Retortamonas intestinalis; Ruminococcusproductus; Serratia liquefaciens; Serratia marcescens; Serratiaodorifera; Streptococcus agalactiae; Streptococcus anginosus;Streptococcus bovis; Streptococcus constellatus; Streptococcusintermedius; Group C+G Streptococci; Succinivibrio dextrinosolvens;Sutterella spp.; Tissierella praeacuta; Veillonella spp.; Aerobacterspp.; Bacillus anthracis; Bacillus cereus; other Bacillus spp.; Borreliarecurrentis; Brucella spp.; Campylobacter coli; Campylobacter fetus;Campylobacter jejuni; Campylobacter sputorum; Clostridium bifermentans;Clostridium botulinum; Clostridium difficile; Clostridium indolis;Clostridium mangenolii; Clostridium perfringens; Clostridium sordellii;Clostridium sporogenes; Clostridium subterminale; Edwarsiella tarda;Francisella tularensis; Listeria monocytogenes; Mycobacterium bovis;Mycobacterium tuberculosis; Pediococcus spp.; Plesiomonas shigelloides;Rickettsia rickettsiae; Salmonella spp.; Shigella boydii; Shigelladysenteriae; Shigella flexneri; Shigella sonnei; other Spirillum spp.;Streptococcus zooepidemicus; Tropheryma whipplei; Vibrio cholerae;Vibrio fluvialis; Vibrio fumissii; Vibrio hollisae; Vibrioparahaemolyticus; Yersinia enterocolitica; Yersinia pseudotuberculosis;Herpes Simplex virus (1 and 2); Cytomegalovirus; Adenovirus;Orthoreoviruses; Rotaviruses; Alphaviruses; Coronaviruses; Toroviruses;Human metapneumovirus; Vesicular stomatitis virus; Machupo virus; Juninvirus; Poliovirus; Coxsackieviruses; Echoviruses; Hepatitis A virus;Noroviruses and other Caliciviruses; Astroviruses; Picobirnaviruses; andHepatitis E virus.

In alternative aspects, the invention may involve the treatment of anIBD with formulations wherein the pathogen is selected from the group ofcommon small and larger bowel pathogens, for example the groupconsisting of: Escherichia coli, Clostridium difficile, Bacteroidesfragilis, Bacteroides vulgatus, Bacteroides thetaiotaomicron,Clostridium perfringens, Salmonella enteriditis, Yersiniaenterocolitica, Shigella flexneri; adenoviruses, astroviruses,caliciviruses, noroviruses, rotaviruses, and cytomegalovirus.

In selected embodiments, the invention involves diagnostic steps toassess a patient's previous exposure to an organism. For example, thediagnostic steps may include taking a medical history of exposure toselected pathogens, and/or evaluating a patient's immune response to aselected pathogen. For example, a serology test may be conducted todetect antibodies to selected pathogens in a patient's sera. Inconnection with this aspect of the invention, antigenic determinants ofa selected pathogen may be chosen for use in an immunogenic compositionon a selected patient based on a diagnostic indication that the patienthas had one or more prior exposure(s) to the pathogen, for example byvirtue of the presence of antibodies to antigenic determinants of thatpathogen in the patient's sera.

In further selected embodiments, the invention involves diagnostic stepsto assess a patient's immunological response to treatment with aselected immunogenic composition. For example, the diagnostic steps mayinclude evaluating a patient's immune response to the antigenicdeterminants of that immunogenic composition, for example using aserological test to detect antibodies to those antigenic determinants.In connection with this aspect of the invention a treatment with aselected immunogenic composition may be continued if the evaluationindicates that there is an active immunological response to theantigenic determinants of that composition, and the vaccine treatmentmay be discontinued, and an alternative treatment with a differentimmunogenic composition may be initiated, if the evaluation indicatesthat there is not a sufficiently active immunological response to theantigenic determinants of the immunogenic composition.

Although various embodiments of the invention are disclosed herein, manyadaptations and modifications may be made within the scope of theinvention in accordance with the common general knowledge of thoseskilled in this art. Such modifications include the substitution ofknown equivalents for any aspect of the invention in order to achievethe same result in substantially the same way. Numeric ranges areinclusive of the numbers defining the range. The word “comprising” isused herein as an open-ended term, substantially equivalent to thephrase “including, but not limited to”, and the word “comprises” has acorresponding meaning. As used herein, the singular forms “a”, “an” and“the” include plural referents unless the context clearly dictatesotherwise. Thus, for example, reference to “a thing” includes more thanone such thing. Citation of references herein is not an admission thatsuch references are prior art to the present invention. Any prioritydocument(s) and all publications, including but not limited to patentsand patent applications, cited in this specification are incorporatedherein by reference as if each individual publication were specificallyand individually indicated to be incorporated by reference herein and asthough fully set forth herein. The invention includes all embodimentsand variations substantially as hereinbefore described and withreference to the examples and drawings.

In some embodiments, the invention excludes steps that involve medicalor surgical treatment.

The following examples illustrate embodiments of the invention.

Example 1: Clinical Studies Bacterial Compositions

Five killed bacterial compositions have been used to treat a widevariety of cancer types and stages in blinded studies, as follows:

1. The Bayer Corporation MRV™ “Bayer MRV” (Hollister-Steir Laboratories,Spokane, Wash., U.S.A.), containing the following bacterial species:

Organisms per ml Staphylococcus aureus 1200 million  viridans andnon-hemolytic Streptococci 200 million Streptococcus pneumoniae 150million Moraxella (Neisseria) catarrhalis 150 million Klebsiellapneumoniae 150 million Haemophilus influenzae 150 million

This vaccine was produced for the following indications: rhinitis,infectious asthma, chronic sinusitis, nasal polyposis and chronic serousotitis media. Cancer treatment was not indicated as an intended use forthis vaccine. The vaccine also included the following ingredients: 0.4%phenol, 0.9% NaCl, trace amounts of brain heart infusion (beef),peptones, yeast extract, agar, sheep blood, dextrose, and sodiumphosphates.

2. Stallergenes MRV “Stallergenes MRV” (Laboratories des Stallergenes,S.A., Fresnes, France), containing the following:

Organisms per ml Staphylococcus aureus 600 million Staphylococcus albus600 million non-hemolytic Streptococci 200 million Streptococcuspneumoniae 150 million Moraxella (Neisseria) catarrhalis 150 millionKlebsiella pneumoniae 150 million Haemophilus influenzae 150 million

This vaccine was produced for the same indications as the MRV vaccinei.e., recurrent respiratory tract infections, and listed cancer as acontraindication.

As set out below, surprisingly, these MRV vaccines, which contain manycommon lung pathogens, were found to be effective for the treatment oflung cancer.

3. Polyvaccinum Forte (PVF; Biomed S.A., Krakow, Poland), containing thefollowing:

Organisms per ml Staphylococcus aureus 500 million Staphylococcusepidermidis 500 million Escherichia coli 200 million Corynebacteriumpseudodiphtheriticum 200 million Streptococcus pyogenes 100 millionStreptococcus salivarius (viridans Streptococci) 100 millionStreptococcus pneumoniae 100 million Moraxella (Neisseria) catarrhalis100 million Klebsiella pneumoniae 100 million Haemophilus influenzae 100million

This vaccine was produced for chronic and recurrent inflammatoryconditions of the upper and lower respiratory tract and genitourinarytract, including rhinopharyngitis, recurrent laryngitis, tracheitis,bronchitis, otitis media, chronic and recurrent neuralgia of trigeminaland occipital nerve, ischialgia, brachial plexitis, intercostalsneuralgia, chronic cystoureteritis, vaginitis, adnexitis, andendometrium inflammation. Cancer treatment was not indicated as anintended use for this vaccine.

Of note, although the total concentration of bacteria in PVF isidentical to that of the MRVs (Bayer and Stallergenes), patientstypically demonstrated a visible inflammatory immune response tosubcutaneous injection of the PVF composition at a much smaller dosethan the usual dose required to achieve a similar skin response with theMRV composition, indicating that the immune reaction was likelyoccurring to one of the novel components in the Polyvaccinum Fortevaccine, such as E. coli. As set out below, surprisingly, PVF, whichcontains E. coli a common pathogen of the colon, abdomen, kidney,ovaries, peritoneum, liver and pancreas, has been found to be effectivein the treatment of cancers in the colon, abdominal lymph nodes, kidney,ovary, peritoneum, liver and pancreas.

4. Staphage Lysate (Delmont Laboratories Inc., Swarthmore, Pa., USA),containing the following: Staphylococcus aureus

As set out below, surprisingly, Staphage Lysate, which containsStaphylococcus aureus a common pathogen of the breast and bone, wasfound to be effective in the treatment of cancer in the breast and bone.

Administration of MRV, Staphage Lysate and PVF

The bacterial compositions (vaccines) were a suspension of killedbacterial cells and therefore, the suspensions were gently shaken priorto use to ensure uniform distribution prior to withdrawing dose fromvial, and administered subcutaneously three times a week on Mondays,Wednesdays, and Fridays. Patients were advised to continue treatment forat least 6 months. The dose of vaccine required was determined by theadequacy of the immune reaction to the vaccine. Beginning with a verysmall dose (0.05 cc), the dose was gradually increased (by 0.01-0.02 cceach time) until an adequate immune reaction was achieved. This delayedlocal reaction at the injection site appeared within 2-48 hours afterinjection and lasted for up to 72 hours or longer. The goal was toachieve a one to two inch diameter round patch of pinkness/redness atthe injection site, indicating adequate immune stimulation. Once thisreaction was achieved, the dose was maintained at the level required toachieve this reaction. If the reaction was significantly less than twoinches (e.g., half an inch) the dose was increased, if it wassignificantly more than two inches (e.g., three inches), the dose wasdecreased. This local immune reaction generally occurs within the first24 hours after the injection. Patients were asked to check for thisreaction and, if present, to measure or mark it. The maintenance doserequired to achieve an adequate immune reaction varies considerably,depending on the individual's immune response—as little as 0.001 cc forsome people, as much as 2 cc for others. The vaccine must be stored in arefrigerator (2° to 8° C.). The usual site for injection is the upperarms, the thighs or the abdomen. The exact site of each injection wasvaried so that it was not given in sites in which pinkness/redness wasstill present. A known contraindication to the vaccines ishypersensitivity to any component of the vaccine.

A fifth vaccine, a polymicrobial oral vaccine, was used in alternativeaspects of the invention, as follows:

5. Respivax, produced by BB-NCIPD Ltd (Bulgaria). This oral vaccinecontained the following freeze-dried killed bacterial species:

Organisms per mg Streptococcus pneumoniae 25 million Neisseriacatarrhalis 25 million Streptococcus pyogenes 25 million Haemophilusinfluenzae 25 million Staphylococcus aureus 25 million Klebsiellapneumoniae 25 million

Administration of Respivax

The Respivax oral vaccine was produced for the treatment for chronicrespiratory infection, and contains many of the most common respiratorytract pathogens, including many of the most common causes of lunginfection. Patients were treated with a dose of one 50 mg tablet perday, providing the equivalent of 1.25×10⁹ cells of each species perdose. Patients were prescribed the above dose for a continuous period ofat least 6 months.

As set out below, surprisingly, Respivax oral vaccine, which containsmany common lung pathogens, was found to be effective for the treatmentof cancer of the lung.

Example 1A: Cancer of the Lung

This section relates to primary cancer in the lung, or metastases to thelung, treated with microbial pathogens of the lung, such as endogenousrespiratory bacteria flora.

Patients qualified for the lung cancer study if they were initiallydiagnosed with stage 3B or 4-lung (inoperable) cancer. Lung cancerstaging was performed using standard methods as for example described inAJCC: Cancer Staging Handbook (sixth edition) 2002; Springer-Verlag NewYork: Editors: Fredrick Greene, David Page and Irvin Fleming, or inInternational Union Against Cancer: TNM Classification of MalignantTumors (sixth edition) 2002; Wiley-Liss Geneva Switzerland: Editors: L.H. Sobin and C. H. Wittekind. For example, lung cancers may beclassified as follows:

TNM Lung Clinical and Pathological Classification T Primary Tumour

-   TX Primary tumour cannot be assessed, or tumour proven by the    presence of malignant cells in sputum or bronchial washings but not    visualized by imaging or bronchoscopy-   Tis Carcinoma in situ-   T0 No evidence of primary tumour-   T1 Tumour 3 cm or less in greatest dimension, surrounded by lung or    visceral pleura, without bronchoscopic evidence of invasion more    proximal than the lobar bronchus (ie, not in the main bronchus)-   T2 Tumour with any of the following features of size or extent: More    than 3 cm in greatest dimension Involves main bronchus, 2 cm or more    distal to the carina Invades visceral pleura Associated with    atelectasis or obstructive pneumonitis that extends to the hilar    region but does not involve the entire lung-   T3 Tumour of any size that directly invades any of the following:    chest wall (including superior sulcus tumours), diaphragm,    mediastinal pleura, parietal pericardium; or tumour in the main    bronchus less than 2 cm distal to the carina but without involvement    of the carina; or associated atelectasis or obstructive pneumonitis    of the entire lung-   T4 Tumour of any size that invades any of the following:    mediastinum, heart, great vessels, trachea, esophagus, vertebral    body, carina; or tumour with a malignant pleural or pericardial    effusion; or with separate tumour nodule(s) within the ipsilateral    primary-tumour lobe of the lung

N Regional Lymph Nodes

-   NX Regional lymph nodes cannot be assessed-   N0 No regional lymph node metastasis-   N1 Metastasis in ipsilateral peribronchial and/or ipsilateral hilar    lymph nodes and intrapulmonary nodes, including involvement by    direct extension-   N2 Metastasis in ipsilateral mediastinal and/or subcarinal lymph    node(s)-   N3 Metastasis in contralateral mediastinal, contralateral hilar,    ipsilateral or contralateral scalene, or supraclavicular lymph    node(s)

M Distant Metastasis

-   MX Distant metastasis cannot be assessed-   M0 No distant metastasis-   M1 Distant metastasis; includes separate tumour nodule(s) in the    non-primary-tumour lobe (ipsilateral or contralateral)

Stage Grouping on TNM Subsets: Occult carcinoma TX N0 M0 Stage 0 Tis N0M0 Stage IA T1 N0 M0 Stage IB T2 N0 M0 Stage IIA T1 N1 M0 Stage IIB T2N1 M0 T3 N0 M0 Stage IIIA T3 N1 M0 T1 N2 M0 T2 N2 M0 T3 N2 M0 Stage IIIBAny T N3 M0 T4 Any N M0 Stage IV Any T Any N M1

Charts with diagnostic codes 162.9 (lung cancer) and 197 (metastaticcancer) were collected manually and electronically. Information wascollected on these patients, such as date of diagnosis, date of death,and cancer stage. Charts for patients were reviewed to confirm the dateof diagnosis and cancer stage. Patients were excluded from the analysisfor the following reasons: 1) wrong stage; 2) missing data; 3) no chart,or; 4) chart did not reach in time for the data analysis. 20 patientswere excluded from the study because their charts have not arrived yetor there was insufficient information, of which 6 were MRV users. Thestudy group includes 108 patients in total: 50 who took the MRV vaccineand 58 who did not take the MRV vaccine.

Comparison of survival of patients initially diagnosed with stage 3B and4 lung cancer who took MRV with patients who didn't take MRV and withSEER standard survival data for patients initially diagnosed with stage3B and 4 lung cancer (FIG. 1) was as follows:

SEER non-MRV MRV median survival: 5 months 10.5 months 12.5 monthssurvival at 1 year: 25%  45%  58% survival at 3 years: 5% 3% 20%survival at 5 years: 3% 0% 10%

A comparison of survival (as above), including only those patients whotook MRV for at least 2 months (FIG. 2) is as follows: median survival:16.5 months

survival at 1 year: 70%survival at 3 years: 27%survival at 5 years: 15%

Median survival and survival at 1 year, 3 years and 5 years, wassubstantially better in the group that was treated with MRV (containingbacteria which commonly cause lung infection), evidence of theeffectiveness of this vaccine for the treatment of lung cancer. Patientswho were treated with the MRV vaccine for more than 2 months had highersurvival rates, further evidence of the effectiveness of this vaccinefor the treatment of lung cancer.

An alternative analysis was conducted on data that included a patientpopulation to whom the MRV composition was not available, to address aperceived potential for bias caused by sicker patients being more likelyto choose the novel treatment (with MRV) and healthier patients beingpotentially less likely to submit to the use of the antigeniccompositions of the invention. Comparison of survival of MRV patients towhom the MRV composition was available (designated “Lung 1”) to survivalof non-MRV patients to whom the MRV composition was not available(designated “Lung 2”) removes some of this selection bias, providing aclearer and more accurate illustration of the benefit of MRV treatment,as illustrated in FIG. 3.

In some embodiments, particularly striking clinical benefits have beenobtained with antigenic bacterial compositions used in repeated frequentinjections (i.e., three times per week) for a prolonged period oftime—such as at least 2, 3, 4, 5, 6 or 12 months, or 2, 3, 4 or 5 years(in the context of advanced cancer such as inoperable lung cancer, thelonger periods may be most beneficial). Treatments of this kind may becarried out so as to provide sustained, prolonged immune stimulation.When the above analysis is restricted to patients who were treated withMRV for a minimum of 2 months, the survival advantage of MRV treatmentis even more clearly illustrated FIG. 4.

As illustrated in FIG. 4, one-year survival of stage 3B or 4 lung cancerpatients treated with MRV for at least two months was 70%, compared tojust 48% for the non-MRV Lung 2 group and 23% for the SEER databasegroup. 3-year survival of the MRV group was more than 4 times that ofboth the non-MRV patients and the SEER registry. None of the non-MRVgroup in the Lung 2 study survived for 5 years, whereas 15% of patientstreated with MRV for a minimum two-month period were still alive 5 yearsafter diagnosis. In the context of an illness such as inoperable lungcancer that is considered terminal and has a usual 5-year survival rateof only 3% (SEER registry), the above results are extremely encouragingand surprising.

When the analysis of patient data is restricted to patients who weretreated with MRV for at least 6 months, the survival curve is trulyremarkable, as illustrated in FIG. 5. More than 60% of patients werealive at 3 years, more than 10 times the survival in both the non-MRVgroup and the SEER registry. 36% (5 of 14 patients) of patients who weretreated with MRV for at least 6 months were alive 5 years afterdiagnosis, compared with only 3% in the SEER database and 0% in thenon-MRV group. These remarkable results, in the context of a cancerdiagnosis that is considered terminal, are extremely promising andsurprising. Accordingly, in some embodiments, cancers, such as advancedcancers, such as inoperable lung cancer, may be treated over a dosingduration of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 months, 2years, 3 years, 4 years, 5 years, or indefinitely.

Restricting analysis to those patients who were treated with MRV for aminimum period of time (e.g., 6 months) introduces a bias in favour ofthe MRV group, since MRV patients who survived for less than that periodof time are excluded from the group (including those who died beforethey could complete the 6 months of treatment). A detailed statisticalanalysis of this bias, with compensatory exclusion of short-termsurvivors in both the non-MRV and SEER groups, demonstrates that thisbias played a very minor role in the truly remarkable survival advantageof patients who were treated with the MRV for at least 6 months.

In stage 3B lung cancer, cancer is confined to the lungs, and thus, atargeted anti-cancer treatment response may be stimulated, in accordancewith various aspects of the invention, by a vaccine, such as MRV,comprised of lung pathogens. In stage 4 lung cancer, the cancer hasmetastasized to distant organs not amenable to targeted stimulation bylung pathogens in accordance with methods of the invention. Thus, inaccordance with some embodiments, patients with stage 3B lung cancer maybe selected for treatment with MRV vaccine, since all of the cancer isconfined to the lungs and thus, will be targeted by the MRV vaccine.When the analysis of patient data is restricted to patients with stage3B lung cancer, comparison of survival curves even more clearlyillustrates the benefit of MRV treatment. As illustrated in FIG. 11,one-year survival of stage 3B lung cancer patients treated with MRV was76%, compared to just 53% for the non-MRV Lung 2 group and 23% for theSEER database group. 3-year survival of the MRV group was 3 times thatthe non-MRV patients and more than 6 times the SEER registry. None ofthe non-MRV group survived for 5 years, whereas 14% of stage 3B patientstreated with MRV were still alive 5 years after diagnosis. In thecontext of an illness such as inoperable stage 3B lung cancer that isconsidered terminal and has a usual 5-year survival rate of only 5%(SEER registry), the above results are extremely encouraging andsurprising.

As some patients did not have their first visit for many months or evena year or two after diagnosis, their inclusion in the survival curvesskews the curve towards longer survival. In order to determine whetherthis bias influenced the difference in survival curves, survival wasanalysed from date of first visit which excludes this bias, asillustrated in FIG. 12. Comparison of survival curves of stage 3B lungcancer patients in FIG. 12 demonstrates an even greater survival benefitfor MRV treatment than illustrated in FIG. 11, indicating that thebenefit of MRV treatment was partially masked in FIG. 11. As illustratedin FIG. 12, 1-year survival (from date of first visit) of stage 3B lungcancer patients treated with MRV was 57%, compared to only 21% for stage3B patients not treated with MRV. While no stage 3B lung cancer patientsnot treated with MRV survived for 3 years, 3-year survival of stage 3Bpatients treated with MRV was 33% and 5-year survival was 14%, aremarkable and unexpected result.

When analysis was restricted to stage 3B lung cancer patients whosefirst visit was within 3 months of diagnosis, the benefits of earlytreatment with MRV are clearly illustrated. As illustrated in FIG. 13,while all stage 3B lung cancer patients who had their first visit within3 months of diagnosis died within 1 year of diagnosis, 70% of stage 3Blung cancer patients treated with MRV within 3 months of diagnosissurvived for 1 year, 40% survived 3 years and 20% survived 5 years, atruly remarkable survival benefit for early MRV treatment.

One aspect of the invention involves the treatment of primary lungcancers or metastasis to the lung with antigenic compositions thatcomprise antigenic determinants of microbial pathogens that are known tobe lung pathogens, such as exogenous lung pathogens or pathogens thatare members of the endogenous flora of the respiratory system. Forexample, antigenic determinants of the endogenous bacterial respiratoryflora species that most commonly cause infection in the lung (see Table5) may be used to treat primary and metastatic cancers situated in thelung: Streptococcus pneumoniae, Moraxella catarrhalis, Mycoplasmapneumoniae, Klebsiella pneumoniae, Haemophilus influenza. Similarly,common viral lung pathogens from Table 5 may be selected for use in someembodiments. Alternatively, a more exhaustive list of endogenous lungpathogens may be selected from Table 1, based on the pathogenicityinformation provided in Table 2. In further alternative embodiments,viral lung pathogens listed in Table 4 may be used. And in furtheralternative embodiments, exogenous bacterial lung pathogens from Table 3may be used in formulating antigenic compositions of the invention, i.e.selected from the group consisting of: Achromobacter spp., Actinomaduraspp., Alcaligenes spp., Anaplasma spp., Bacillus anthracis, otherBacillus spp., Balneatrix spp., Bartonella henselae, Bergeyellazoohelcum, Bordetella holmesii, Bordetella parapertussis, Bordetellapertussis, Borrelia burgdorferi, Borrelia recurrentis, Brucella spp.,Burkholderia gladioli, Burkholderia mallei, Burkholderia pseudomallei,Campylobacter fetus, Capnoctyophaga canimorsus, Capnoctyophagacynodegmi, Chlamydia pneumoniae, Chlamydia psittaci, Chlamydophilapneumoniae, Chromobacterium violaceum, Chlamydophila psittaci,Chryseobacterium spp., Corynebacterium pseudotuberculosis, Coxiellabumetii, Francisella tularensis, Gordonia spp., Legionella spp.,Leptospirosis spp., Mycobacterium avium, Mycobacterium kansasii,Mycobacterium tuberculosis, other Mycobacterium spp., Nocardia spp.,Orientia tsutsugamushi, Pandoraea spp., Pseudomonas aeruginosa, otherPseudomonas spp., Rhodococcus spp., Rickettsia conorii, Rickettsiaprowazekii, Rickettsia rickettsiae, Rickettsia typhi.

For example, since the MRV compositions contain many of the most commonlung pathogens, these vaccines may be used to treat primary lung canceror lung metastases, as illustrated in the cumulative data presentedhere, and in a number of the case reports. In accordance with theforegoing results, one aspect of the invention involves the treatment ofprimary lung cancer and metastasis to the lung with antigeniccompositions that comprise antigenic determinants of microbial pathogensthat are known to be pathogenic in the lung, such as exogenous lungpathogens or pathogens that are members of the endogenous flora of therespiratory tract. In selected embodiments, antigenic determinants ofthe common lung pathogens may be used to treat primary and metastaticcancers situated in the lung, for example, antigenic determinants fromone or more of the following bacterial species or viral types:Streptococcus pneumoniae, Moraxella catarrhalis, Mycoplasma pneumoniae,Klebsiella pneumoniae, Haemophilus influenza, influenza virus,adenovirus, respiratory syncytial virus, and parainfluenza. In furtherselected embodiments, antigenic determinants of Streptococcuspneumoniae, the most common cause of bacterial lung infection, may beused alone or with other of the most common pathogens of the lung totreat cancer of the lung.

Primary lung cancer may also arise from bronchial tissue and therefore,in some embodiments, antigenic compositions that comprise antigenicdeterminants of microbial pathogens that are known to cause bronchialinfection may be used to treat patients with cancer situated in thebronchial tissue, including, for example, the following common causes ofbronchial infection: Mycoplasma pneumoniae, Chlamydophila pneumoniae,Bordetella pertussis, Streptococcus pneumoniae, Haemophilus influenzae,influenza virus, adenovirus, rhinovirus, coronavirus, parainfluenza,respiratory syncytial virus, human metapneumovirus, or coxsackievirus.Lung cancer (or lung metastases) that is located in both lung andbronchial tissue may be treated with antigenic compositions thatcomprise antigenic determinants of microbial pathogens that are known tocause both lung and bronchial infection (for example, Streptococcuspneumoniae, Haemophilus influenza and Mycoplasma pneumoniae are allcommon lung and bronchial pathogens) or alternatively, with antigeniccompositions that comprise antigenic determinants of microbial pathogensthat are known to cause lung infection and antigenic determinants ofmicrobial pathogens that are known to cause bronchial infection.

Example 1B: Breast Cancer with Metastasis to the Bone or Lung

The most common cause of both breast infection and bone infection isStaphylococcus aureus. Accordingly, in one aspect of the invention, anantigenic composition comprising antigenic determinants of S. aureus maybe used to treat breast cancer with metastases to the bone. Theremarkable case of Patient R (PtR), treated with a Staphylococcus aureusvaccine, set out below in the Case Reports, illustrates the efficacy ofthis approach to treating breast cancer with bone metastases. Asillustrated in FIG. 6, in a cumulative series of 52 patients, survivalof breast cancer patients with metastases to bone and/or lung treatedwith MRV (n=19), which contains Staphylococcus aureus, was better thanthe survival of patients not treated with the MRV vaccine (n=33):

% survival MRV patients % survival non-MRV patients 10 months 95% 76% 20months 74% 61%  5 years 26% 18%

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of primary cancer in the breast or metastasis tothe breast with antigenic compositions that comprise antigenicdeterminants of microbes that are known to cause breast infection, andtreatment of primary cancer of the bone or metastasis to the bone withantigenic compositions that comprise antigenic determinants of bacterialspecies or viruses that are known to cause bone infection. In selectedembodiments, a vaccine comprising antigenic determinants ofStaphylococcus aureus, the most common cause of both breast and boneinfection, may be used alone or in combination with other of the mostcommon pathogens of the breast to treat cancer in the breast, or aloneor in combination with other of the most common pathogens of the bone totreat cancer in the bone.

Example 1C: Metastases to the Bone

One of the most common sites for metastases in patients with prostatecancer is bone. In one aspect of the invention, the MRV composition,which contains antigenic determinants of S. aureus, the most commoncause of bone infection, may be used for the treatment of metastases tothe bone, for example in patients who have, or who have had, a primaryprostate cancer. The graph of FIG. 7 is a comparison of survival of acumulative series of metastatic prostate cancer patients who had surgeryor radiation to destroy their prostate gland (and thus, the primarytumour) and who had detectable cancer limited to bone metastases. Asillustrated, the survival of patients treated with MRV (n-4) issubstantially better than that of patients not treated with MRV (n=7):

% survival MRV patients % survival non-MRV patients 2 years 100%  57% 3years 75% 43% 5 years 50%  0%

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of primary bone cancers or metastases to the bonewith antigenic compositions that comprise antigenic determinants ofmicrobial pathogens that are known to cause bone infection, such asexogenous bone pathogens or pathogens that are members of the endogenousflora of the skin, mouth or colon. For example, in selected embodiments,antigenic determinants of one or more of the following microbial speciesfrom the list of common bone pathogens may be used to treat primary andmetastatic cancers situated in the bone: Staphylococcus aureus,coagulase-negative staphylococci, Streptococcus pyogenes, Streptococcuspneumoniae, Streptococcus agalactiae, other streptococci spp.,Escherichia coli, Pseudomonas spp., Enterobacter spp., Proteus spp.,Serratia spp., parvovirus B19, rubella, hepatitis B. In further selectedembodiments, Staphylococcus aureus, the most common cause of boneinfection, may be used alone or with other of the most common pathogensof the bone to treat cancer of the bone.

Example 1D: Cancer Situated in the Colon

Treatment with the PVF composition has been shown to improve thesurvival of colon cancer patients (see FIG. 8), as illustrated by acomparison of the following four colon cancer patient groups:

-   -   Stage 4 colon cancer patients who were treated with MRV.    -   Stage 4 colon cancer patients who were not treated with a        vaccine.    -   Stage 4 colon cancer patients who were treated with PVF vaccine.    -   Stage 4 colon cancer patients from the SEER (Surveillance,        Epidemiology and End Results) database.

This example illustrates that patients with colon cancer treated withPVF, which contains E. coli the most common cause of bacterial infectionof the colon, have substantially improved survival.

Patients qualified for the first two groups of this study if theypresented with stage 4 colon cancer. Patients were excluded from thisanalysis for the following reasons:

-   -   incorrect diagnosis    -   incorrect stage    -   missing essential data (e.g., date of death)    -   no chart    -   chart did not reach us in time for the data analysis.

The patient group included a total of 136 stage 4 colon cancer patients:15 who took the PVF vaccine, 56 who took the MRV vaccine, and 65 who didnot take a vaccine. Results are illustrated in FIG. 8, as follows:

SEER no vaccine MRV PVF median survival: 8.4 mo. 15.1 mo. 15.0 mo. 33.6mo. at 10 months 45% 69% 71% 100%  at 20 months 24% 42% 36% 67% at 30months 14% 29% 23% 52% at 5 years  5%  6%  7% 10%

The median survival of patients with stage 4 colon cancer treated withPVF (which contains E. coli, one of the most common colonic pathogens)was more than double that of patients treated with MRV (which does notcontain colonic pathogens) or patients not treated with a vaccine, andfour times that of the SEER registry. All 15 patients treated with PVFwere still alive 10 months after diagnosis, compared to only 71% for theMRV group, 69% for the no-vaccine group and only 45% for the SEERregistry. Survival at 30 months for the PVF group was double that ofboth the MRV group and the no-vaccine group and almost 4 times that ofthe SEER registry.

The wilcoxon test shows a statistically significant survival differencebetween patients treated with PVF vaccine and both the MRV group(p=0.0246) and the no vaccine group (p=0.0433). This is remarkableconsidering the small size of the PVF group (n=15), indicative ofsubstantial therapeutic effect. As evidenced by these results, the PVFcomposition, which contains E. coli the most common cause of bacterialinfection of the colon, is an effective treatment for colon cancer.

Survival of those patients who presented for immunological treatment inaccordance with the invention within 3 months of diagnosis (i.e.,excluding those patients who were long-term survivors before presentingfor treatment) has also been analyzed. The results of this analysis arepresented in FIG. 9. As illustrated, the ‘MRV’ and ‘No Vaccine’ survivalcurves in FIG. 9 are shifted substantially to the left (indicating thata selection bias towards ‘long-term’ survivors may have artifactuallyshifted these curves to the right in FIG. 8), whereas, remarkably, thePVF curve in FIG. 9 is actually further to the right than the curve inFIG. 8, indicating that the benefit of earlier treatment with PVF (i.e.,within 3 months of diagnosis) more than outweighed any long-termsurvivor bias excluded in FIG. 9. This analysis provides compellingevidence that the benefit of PVF treatment for stage 4 colon cancer maybe even greater than that illustrated in FIG. 8, and that the earlierthe treatment with the compositions of the invention is begun followingdiagnosis, the greater the benefit.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of colon cancers with antigenic compositions thatcomprise antigenic determinants of microbial pathogens that are known tobe colon pathogens, such as pathogens that are members of the endogenousflora of the colon or exogenous colonic pathogens. For example,antigenic determinants of the following microbial species may be used totreat primary and metastatic cancers situated in the colon: Escherichiacoli, Clostridium difficile, Bacteroides fragilis, Bacteroides vulgatus,Bacteroides thetaiotaomicron, Clostridium perfringens, Salmonellaenteriditis, Yersinia enterocolitica, Shigella flexneri; adenoviruses,astroviruses, caliciviruses, noroviruses, rotaviruses, orcytomegalovirus. For example, cancers situated in the colon may betreated with the PVF composition, which contains E. coli, or alternativeformulations that include only antigenic determinants of colonicpathogens. In selected embodiments, antigenic determinants of E. coli,the most common bacterial cause of colon infection, may be used alone orwith antigenic determinants of other common pathogens of the colon totreat cancer of the colon.

Example 1E: Use of Respivax, an Oral Vaccine to Treat Lung Cancer

Oral Respivax vaccine was administered as described above, with a doseof one 50 mg tablet per day, providing the equivalent of 1.25×10⁹ cellsof each species per dose. Patients were advised to continue the abovedose for at least 6 months.

As illustrated in FIG. 10, survival of stage 3B lung cancer patients whowere treated with the oral Respivax antigens was substantially betterthan patients who were not treated with the antigenic composition.Median survival was 37 months for the patients treated with Respivax,compared to only 20 months for those patients not treated with anantigenic composition vaccine. 40% of patients treated with Respivaxwere alive 5 years after diagnosis, whereas none of the untreatedpatients survived for more than 2 years.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of primary of the lung or metastases to the lungwith oral administration of antigenic compositions that compriseantigenic determinants of microbial pathogens that commonly cause lunginfection.

Example 2: Case Reports

These case reports are indicative of the patients that make up thepatient populations reflected in the foregoing cumulative studies, aswell as illustrating additional aspects of the invention. In particular,the individual case reports of Patients A-N are illustrative ofsurprising results in some patients being treated withanti-inflammatories, while the case reports of Patients O-AA arerepresentative of the general patient population that includes manyexamples of vaccine treatment that was effective in the absence ofanti-inflammatory therapy.

MRV for Cancer of the Lung with and without Anti-Inflammatories

Patient A (PtA): In September year 0, PtA developed right upper chestpain with an associated wheeze. These symptoms persisted and in January,year 1, she had a chest x-ray that revealed a large 7 cm×8 cm mass inthe apex of the right lung. A fine needle aspiration was positive fornon-small cell lung cancer. On January 27, year 1, an MRI showedinvasion of the subclavian arteries, making surgical resectionimpossible and thus, PtA was diagnosed with stage 3B inoperable terminallung cancer. She underwent a short course of palliative radiation anddeclined chemotherapy. She was told that she had terminal cancer with a3 to 6 months life expectancy.

On April 29, year 1, PtA began therapy with MRV vaccine three times perweek. On that same date she also began treatment with the non-steroidalanti-inflammatory agent (NSAID) indomethicin 50 mg four times per dayand a regime of antioxidant supplements and vitamin D. 18 months later,by October, year 2, the tumour had markedly reduced in size to 3 cm indiameter and, by May 19, year 5, four years after starting treatmentwith the combined regime of MRV vaccine, indomethicin, antioxidantsvitamins and vitamin D, only residual scarring remained. PtA continuedtreatment with this combination of MRV vaccine and adjuvantanti-inflammatory therapies for more than 4 years until the end of May,year 5 at which time there was no evidence of residual cancer, in spiteof a diagnosis of terminal inoperable lung cancer more than 4 yearspreviously. More than 14 years since diagnosis with terminal lungcancer, PtA continues to feel well with no evidence of residual cancer.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of cancers in the lung with administration ofantigenic compositions that comprise antigenic determinants of microbialpathogens that commonly cause lung infection.

In accordance with the forgoing results, another aspect of the inventioninvolves the administration of the immunogenic compositions repeatedlyrelatively frequently over a relatively long period of time.

The concomitant use of anti-inflammatory agents, such as antioxidants,vitamin D and indomethicin, in conjunction with targeted MRV therapy,was associated with substantially improved survival, which was greaterthan that of otherwise similar cases, in which these adjuvantanti-inflammatory modalities were not used in conjunction with thecompositions of the invention. For example, Patient B, an otherwisesimilar case in which anti-inflammatories were not administered, wasdiagnosed with inoperable stage 3B non-small cell lung cancer, which wasfatal within 3 months of diagnosis. These cases provide evidence of asynergistic effect between the antigenic compositions of the inventionand anti-inflammatory treatments.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of cancers with both the administration ofantigenic compositions that comprise antigenic determinants of microbialpathogens that are pathogenic to the organ or tissue targeted, as wellas adjuvant anti-inflammatory treatments, for synergistic effect.

MRV for Cancer of the Lung with and without Anti-Inflammatories

Patient C (PtC): In the spring of year 0, PtC began having pain in hisright upper chest area. This pain persisted and on October 5, year 0 hehad a chest x-ray that revealed a large 12 cm×11 cm mass occupyingvirtually the entire right upper lobe. A fine needle aspiration waspositive for poorly differentiated non-small cell lung cancer.Exploratory thoracotomy was performed on December 7, year 0, whichrevealed tumour invasion of the chest wall and superior vena cava andtherefore, PtC's tumour was inoperable (i.e., stage 3B). PtC underwent ashort course of palliative radiation and declined chemotherapy. He wastold that he had terminal cancer with a 3 to 6 months life expectancy.By January 27, year 1, the rapidly growing tumour had increased in sizeto 14 cm×11.5 cm.

On February 9, year 1, PtC began treatment with indomethicin 50 mg fourtimes per day, antioxidant vitamins, and vitamin D. Three weeks later,on March 1, year 1, PtC began treatment with MRV vaccine three times perweek. By June, year 1, PtC was feeling well and was running 8 km 3-4times per week. On June 4, year 1, a chest x-ray revealed that thetumour had reduced in size to 11 cm diameter. PtC continued to feel verywell, leading a full and active life with return to full employment andcontinued full physical activity. PtC continued treatment with acombination of the MRV vaccine and adjuvant anti-inflammatory therapies(indomethicin, antioxidants and vitamin D) for more than 16 months untilJuly 24, year 2, at which time indomethicin treatment was discontinued(as a result of decreased kidney function, a known potential side-effectof long-term indomethicin use). 6 months later, in December, year 2,after 22 months of targeted vaccine therapy, MRV treatment wasdiscontinued (since MRV was no longer available past that date). PtCcontinued to feel well until June, year 6, at which time he wasdiagnosed with a recurrence of cancer in both lungs, which lead to hisdeath on May 26, year 7, more than 6.5 years after he was diagnosed withterminal lung cancer and told he had 3-6 months to live.

In this case, the use of adjuvant anti-inflammatory agents, includingantioxidants, vitamin D and indomethicin, used in conjunction withtargeted MRV therapy for more than 16 months, was associated withsubstantially improved survival in the face of a diagnosis that isusually fatal within 1 year, which was greater than that of an otherwisesimilar case, Patient D, in which these adjuvant anti-inflammatorymodalities were not used in conjunction with the compositions of theinvention, and an inoperable lung cancer was fatal within 8 months ofdiagnosis. These cases provide evidence of a synergistic effect betweenthe antigenic compositions of the invention and anti-inflammatorytreatments.

PVF for Cancer of the Colon with Metastases to the Liver and Lung, andwithout Anti-Inflammatories

Patient E (PtE): PtE had a surgical resection of colon cancer on June17, year 0, followed by chemotherapy. On August 15, year 0, he wasdiagnosed stage 4 cancer with metastases to the liver and lungs, adiagnosis with a very poor prognosis. On October 20, year 0, PtE begantreatment with an antioxidant and vitamin D regime and, on December 10,year 0, he began treatment with the PVF composition three times perweek, which he has continued in combination with the antioxidants andvitamin D. In September, year 1, he began treatment with Celebrex™ 100mg twice per day. In spite of a very poor initial prognosis, PtE wasstill and feeling well at last contact, more than 3 years afterdiagnosis with terminal metastatic colon cancer.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of cancers of the colon, liver and lung withadministration of antigenic compositions that comprise antigenicdeterminants of microbial pathogens that are known to be pathogenic inthe colon, liver and lung.

In contrast to PtE, of the 15 patients diagnosed with stage 4 coloncancer and treated with PVF, the patient with the shortest survival,Patient F, was not treated with anti-inflammatories. These cases providecompelling evidence that anti-inflammatory modalities (i.e., Celebrex™,anti-oxidants and vitamin D) taken in conjunction with targeted PVFtherapy has a synergistic effect, contributing to PtE's prolongedsurvival, which was greater than that of otherwise similar cases inwhich these adjuvant anti-inflammatory modalities were not used inconjunction with the compositions of the invention.

PVF for Cancer of the Colon with Metastases to Lung, withAnti-Inflammatories

Patient G (PtG): PtG developed rectal bleeding in May, year 0, and wasdiagnosed with colon cancer. He underwent surgery, chemotherapy andradiation, but developed metastases to his lungs (stage 4 cancer) on 16August, year 1, a terminal diagnosis with a poor prognosis. He had beguna regime of antioxidant vitamins and vitamin D in June, year 0, and, onSeptember 23, year 1, he began taking the NSAID Celebrex 100 mg twiceper day. In March, year 3, he began PVF vaccine three times per week,which he continued till April, year 4 at which time he developed brainmetastases, which lead to his death on June 2, year 4, almost 3 yearsafter a diagnosis of stage 4 terminal colon cancer. PtG livedsubstantially longer than would normally be expected with a diagnosis ofstage 4 colon cancer with metastases to the lungs. In this context, theinvention provides for the use of anti-inflammatory modalities inconjunction with immunogenic compositions, such as PVF, for synergisticeffect.

Patient H (PtH): PtH was diagnosed with colon cancer with metastases tothe liver and lungs on February 13, year 0. On January 11, year 1, hewas prescribed an antioxidant and vitamin D regime. However, in March,year 1, he entered a chemotherapy research study and discontinued thesesupplements at that time at the request of the study coordinators. Hewas not treated with any NSAIDs. On May 12, year 1, he began treatmentwith PVF, which he took three times per week until his death just 2.5months later. When contrasted to similar cases that involved the use ofanti-infammatories, this case illustrates that, if adjuvantanti-inflammatory modalities are not given concomitantly with thetargeted antigenic activation therapy, there is a lack of a synergisticeffect that would otherwise occur with concomitant use of adjuvantanti-inflammatory modalities.

In summary, in cases of stage 4 colon cancer treated with targeted PVFvaccine therapy, the use of adjuvant anti-inflammatory agents, includingantioxidants, vitamin D and Celebrex, used in conjunction with targetedantigenic activation therapy, was associated with substantially improvedsurvival, much greater than that of the two cases in which theseadjuvant anti-inflammatory modalities were not used in conjunction withthe vaccine, providing evidence suggestive of a synergistic effect.

PVF with and without Anti-Inflammatories for Cancer of the Pancreas withMetastases to the Lungs, Liver and Abdominal Lymph Nodes

Patient I (PtI): PtI was diagnosed with pancreatic cancer in August,year 1, at which time he had surgery to remove his pancreas (i.e.,Whipple's procedure). However, in July year 2, he developed metastasesto the lungs bilaterally and in February year 4 he developed recurrenceof cancer in the pancreatic area with abdominal and liver metastases.This is a terminal diagnosis with a very poor prognosis. PtI began aregime of antioxidant vitamins, vitamin D, large doses of turmeric(curcumin), fish oil (9 gm per day), resveratrol and green tea(equivalent of 36 cups per day) on September 27, year 2, all of whichare anti-inflammatory modalities, all of which he continued to take. InMarch year 3, he began treatment with Celebrex 100 mg twice per day,which he took for more than 20 months. PtI began treatment with PVFthree times per week in May year 4, which he has continued to useregularly for more than 3 years. PtI survived for 5 years after adiagnosis of terminal metastatic pancreatic cancer, a remarkablyprolonged survival in the context of a diagnosis that has an extremelypoor prognosis. This case provides evidence that high doses of multipleanti-inflammatory modalities (i.e., Celebrex, antioxidants, vitamin D,turmeric, fish oil, resveratrol, green tea) taken in conjunction withthe PVF compositions, resulted in a synergistic effect which hascontributed to PtI's remarkable survival for 5 years after developingmetastatic pancreatic cancer, a diagnosis that is usually fatal within 6months.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of cancer of the pancreas, abdominal lymph nodes,liver and lung with administration of antigenic compositions thatcomprise antigenic determinants of microbial pathogens that are known tocause infection in the pancreas, abdominal lymph nodes, liver and lungs.

Patient J (PtJ) had an essentially identical diagnosis to PtI (i.e.,pancreatic cancer with metastases to abdominal lymph nodes, lungs andliver). PtJ, who did not take any other anti-inflammatories along withthe PVF vaccine except antioxidants and vitamin D, died within 4 monthsof diagnosis, whereas PtI, who took large doses of numerous otheranti-inflammatories modalities (i.e., Celebrex, turmeric, fish oil,resveratrol and green tea) in conjunction with PVF vaccine, survived for5 years after diagnosis. These cases provide evidence of a synergisticeffect of high dose multiple anti-inflammatory modalities and targetedvaccine therapy.

MRV for Cancer of the Breast with Metastases to the Bone

Patient K (PtK): In March, year 0, PtK developed neck and back pain,which persisted. On July 28, year 0, she was diagnosed with stage 4breast cancer with metastases to the cervical spine, an incurablediagnosis. She underwent surgery to remove two breast lumps (axillarylymph nodes positive) and palliative radiation to the metastases in herspine. On January 18, year 1, PtK began treatment with doses ofantioxidants and vitamin D, as well as the NSAID indomethicin 50 mg fourtimes per day. Three days later, on January 21, year 1, she begantreatment with the MRV composition, which contains Staphylococcus aureusthe most common pathogen of both the breast and bone. Although there wasno documentation of the exact length of time that treatment with thiscombination of MRV/indomethicin/antioxidant/vitamin D was continued, thepatient was given sufficient vaccine (20 ml) for approximately 2 yearsof treatment at the usual dose and frequency (i.e., three times perweek) and PtK stated that she completed the recommended treatment courseat home. Remarkably, PtK was still alive at last contact, 13 years afterdiagnosis with stage 4 metastatic breast cancer with metastases to bone.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of cancers of the breast and bone withadministration of antigenic compositions that comprise antigenicdeterminants of microbial pathogens that are known to be pathogenic inthe breast and bone infection.

In contrast to Patient K, Patient L (PtL) was diagnosed with breastcancer with metastases to bone on October 11, year 0. She was notprescribed an NSAID or other anti-inflammatories. PtL began treatmentwith MRV on February 27, year 1. She died 9 months later on November 4,year 1, just over one year after diagnosis with stage 4 breast cancerwith metastases to bone. The contrast between the otherwise similarcases of PtK and PtL illustrates the potential for synergistic treatmentwith anti-inflammatories and the antigenic compositions of theinvention.

MRV with and without Anti-Inflammatories for Cancer of the Breast withMetastases to the Bone

Patient M (PtM): PtM was diagnosed with stage 4 breast cancer withmetastases to bone on June 15, year 0. She began on the NSAID Naprosyn250 mg twice per day on an ongoing basis for pain relief and, inOctober, year 3, she began doses of antioxidants and vitamin D. Threemonths later, on January 15, year 4, she began treatment with MRVvaccine (which contains Staphylococcus aureus, the most common breastand bone pathogen) in combination with these anti-inflammatory therapies(i.e., Naprosyn, antioxidants and vitamin D). PtM lived for more than 9years after being first diagnosed with stage 4 metastatic breast cancerwith metastases to bone, an unusually long survival considering theusual poor prognosis associated with this diagnosis.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of cancers of the breast and bone withadministration of antigenic compositions that comprise antigenicdeterminants of microbial pathogens that are known to be common causesof breast and bone infection.

In contrast to PtM, Patient N (PtN): PtN was diagnosed with stage 4cancer with metastases to bone on April 8, year 0. She began doses ofantioxidants and vitamin D on April 24, year 0. However, prior tostarting MRV, she was prescribed the blood thinner warfarin, limitingsupplementation with vitamin E and vitamin C, two important antioxidantsthat can lead to potential complications if used in conjunction withwarfarin. In addition, NSAIDs could not be prescribed in this case sincethey are contraindicated with warfarin use. On June 2, year 1 PtN begantreatment with MRV. She died 14 months later in August, year 2. In thiscontext, it is possible that the use of targeted vaccine therapy withoutthe synergistic effect of adjuvant anti-inflammatories (i.e., NSAID,vitamin E and therapeutic doses of vitamin C) limited its potentialbenefit.

In summary, in the cases of stage 4 breast cancer with metastases to thebone treated with targeted MRV therapy detailed above, the use ofadjuvant anti-inflammatory agents in conjunction with MRV was associatedwith substantially improved survival, much greater than that of the twocases in which these adjuvant anti-inflammatory modalities were not usedin conjunction with the vaccine, providing evidence suggestive of asynergistic effect.

MRV for Metastases to the Lungs

Patient O (PtO) was diagnosed in June, year 0 with kidney cancer withmetastases to the lungs bilaterally and to the bone (left femur). Thisis generally considered to be an incurable terminal diagnosis with apoor prognosis. He began treatment with the MRV on August 10, year 0 andcontinued regular treatment (three times per week) for 16 months (afterwhich MRV was no longer available). In September, year 0, he began 7months of treatment with an experimental drug, pegylated interferonalpha-2a. His left femur was ‘pinned’ due to the risk of fracture as aresult of the metastasis but, due to surgical complications, amputationof the left leg below the mid-thigh was required. In September, year 2,his cancerous right kidney was removed. In October, year 2, a PET scanfound no evidence of cancer in the lungs and no further evidence of bonemetastases. PtO is alive with no evidence of cancer in his lungs, morethan 9 years after a diagnosis of bilateral pulmonary metastases, aremarkable result.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of metastases to the lung with administration ofantigenic compositions that comprise antigenic determinants of microbialpathogens that are known to be lung pathogens.

MRV for Metastases to the Bone and Lungs

Patient P (PtP) was diagnosed with kidney cancer in July, year 0, andunderwent excision of this right kidney. In December, year 4, hedeveloped metastases to the bone (femurs bilaterally) and lungs(bilaterally). PtP declined conventional treatment and began treatmentwith MRV in April, year 5, which he continued regularly, three times perweek, for 18 months. PtP's health improved and he returned to normaldaily activities. X-rays and imaging of the chest and femurs showed noprogression, with stable disease in the lungs and femurs during the 18months that PtP was on MRV treatment.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of metastases to the lung and bone withadministration of antigenic compositions that comprise antigenicdeterminants of microbial pathogens that are common causes of lung andbone infection.

MRV for Metastases to the Lungs

Patient Q (PtQ) was diagnosed with colon cancer with probable metastasesto the lungs in June, year 0. At that time, the primary colon tumour wasfully excised, leaving only several lung metastases. PtQ startedtreatment with MRV on December 11, year 0 which she continued threetimes per week for 4 months. On April 19, year 1, after 6 monthstreatment with chemotherapy, she had surgery to excise the only visiblelung lesion remaining, which was confirmed to be a metastatic lesion. Adiagnosis of colon cancer with lung metastases has a poor prognosis,even in the context of chemotherapy followed by surgery to excisevisible metastases. In spite of her original poor prognosis, PtQ remainsin excellent health, with no evidence of cancer more than 10 years afterher initial diagnosis with metastases to the lung and treatment withMRV.

S. aureus Antigens for Breast Cancer with Metastasis to the Bone

Patient R (PtR): In May, year 0, PtR was diagnosed with breast cancerwith metastases to her sternum, femur and cervical spine, an incurablecancer with a poor prognosis. She was treated with radiation andTamoxefen. In May, year 4, she developed an additional area ofmetastasis in her lumbar spine and she began on treatment with Megace.In November, year 4, she began treatment with a vaccine (StaphageLystate vaccine) containing only Staphylococcus aureus, the most commoncause of infection of both the breast and bone and thus, a selectedformulation for the treatment of breast and bone cancer. She continuedregular therapy with this vaccine for 5 years. In spite of a diagnosisof metastatic breast cancer with multiple bone metastases, PtR survivedfor more than 17 years, a remarkable survival in the context ofincurable metastatic breast cancer and a testament to the promise oftargeted vaccine therapy for the treatment of breast cancer.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of cancers of the breast and bone withadministration of antigenic compositions that comprise antigenicdeterminants of microbial pathogens that are known to be the most commoncause of the breast and bone infection.

This embodiment illustrates that a formulation that includes antigenicdeterminants of only the most frequently pathogenic organism ororganisms for a tissue may provide particular advantages, as is alsoillustrated in the mouse model data set out below. In keeping with this,we have found enhanced effectiveness of Respivax as opposed to MRV intreating cancers situated in the lung, reflecting the fact that theRespivax formulation is somewhat more optimal because it includes higherrelative concentrations of the pathogenic species which most commonlycause lung infection (i.e., 67% of the bacterial cell count of Respivaxis comprised of species that most commonly cause lung infection, whereasonly 30% of the MRV vaccines are comprised of species that most commonlycause lung infection).

In accordance with the foregoing results, one aspect of the inventioninvolves formulating the antigenic compositions such that antigenicdeterminants of microbial pathogens that are known to be the commoncauses of infection are given preferential priority in the proportionsof the formulation, with the most common cause of infection receivingthe greatest preferential priority. For example, the proportion ofantigenic determinants that are derived from pathogens that are known tobe a common cause of infection may be 10%, 20%, 30%, 40%, 50%, 60%, 70%,80%, 90%, 95% or 100%.

Accordingly, in some embodiments, the invention provides antigeniccompositions in which a threshold proportion of antigenic determinantsselected in accordance with the invention are used, relative to anyother antigenic determinants in the composition. For example, antigeniccompositions may have greater than X % of the antigenic determinantstherein derived from pathogenic (or commonly pathogenic, or mostcommonly pathogenic) species, where X may for example be 10, 20, 30, 40,50, 60, 70, 80, 90, 95 or 100 (or any integer value between 10 and 100).For example, at least X % of the antigenic determinants in the antigeniccomposition may be specific for microbial pathogens that are pathogenic(or commonly pathogenic, or most commonly pathogenic) in the specificorgan or tissue of the patient within which the cancer is situated.Using an alternative measure, of the total number of microbial pathogensin the antigenic composition, at least X % may be selected to bemicrobial pathogens that are pathogenic (or commonly pathogenic, or mostcommonly pathogenic) in the specific organ or tissue of the patientwithin which the cancer is situated. In some embodiments, the antigeniccomposition may accordingly consist essentially of antigenicdeterminants of one or more microbial pathogens that are each pathogenicin the specific organ or tissue within which the cancer is situated. Inselected embodiments, the antigenic composition may consist essentiallyor entirely of antigenic determinants of microbial pathogens that arecommonly pathogenic in the specific organ or tissue of the patients withwhich the cancer is situated. In further selected embodiments, theantigenic composition may consist essentially or entirely of antigenicdeterminants of a microbial pathogen (or pathogens) that are mostcommonly pathogenic in the specific organ or tissue of the patients withwhich the cancer is situated.

In the context of various aspects of the invention, organisms arecharacterized by the frequency with which they are pathogenic. In thiscontext, the invention also relates to the frequency with whichendogenous flora are pathogenic. For clarity, in this regard, thecharacterizations herein of the frequency of pathogenicity, such as thedesignation “commonly pathogenic” relate, in general, to the proportionof infections in a particular organ or tissue that are commonlyattributed to a particular organism, and not to the frequency with whichmicrobial colonization of a tissue is converted to a pathogenicinfection. In North America, the majority of human infections areunderstood to be caused by endogenous organisms, even though theseorganisms commonly are present as part of the endogenous flora withoutcausing infection. For example, while S. pneumonia is a common cause oflung infection (i.e., pneumonia) in humans (and thus, is designated“commonly pathogenic” in the lung), it is nevertheless also true that S.pneumoniae is commonly present as part of the endogenous flora of therespiratory tract without causing infection and thus, in the nature ofan endogenous colonization, is not normally pathogenic.

MRV for Multiple Myeloma

Patient S (PtS) was diagnosed with multiple myeloma (stage 3A) in thefall of year 0, with multiple lesions on bone scan, including skull,humeri and pelvis. He was treated with standard chemotherapy (melphalanand prednisone) for 6 months. However, in December year 3, he developeda pathological fracture of his right femur as a result of his disease,which required pinning and local radiation. On April 28, year 4, PtSbegan treatment with MRV, which contains Staphylococcus aureus a commoncause of septicemia, which he continued for more than 13 years untilthis vaccine was no longer available in December year 17. Remarkably,PtS is still alive almost 25 years after being diagnosed with multiplemyeloma, a truly extraordinary outcome considering his ‘terminal’diagnosis.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of hematological cancers with administration ofantigenic compositions that comprise antigenic determinants of microbialpathogens that are known to cause septicemia.

In accordance with the forgoing results, and as illustrated in otherpatient case reports detailed herein, another aspect of the inventioninvolves the administration of the immunogenic compositions repeatedlyrelatively frequently over a relatively long period of time, asdescribed elsewhere herein.

PVF for Colon Cancer with Metastases of the Liver and Abdominal LymphNodes

Patient T (PtT) was diagnosed with colon cancer and was treated withexcision of the primary tumour (and subsequent chemotherapy) inSeptember year 0. Ten months later, she developed a liver metastasis,which was surgically excised in July year 1. PtT remained well untilJune year 7, when she was diagnosed with recurrent disease—an inoperablemass of abdominal lymph nodes in close proximity to the aorta and spine,obstructing her left ureter, requiring insertion of a nephrostomy tube.PtT was considered terminal and treated with palliative radiation inOctober year 7. She began treatment with PVF on November 17, year 7,which she continued every second day. PtT survived for almost 4 yearsafter being diagnosed with terminal recurrent metastatic colon cancer.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of cancer in abdominal lymph nodes withadministration of antigenic compositions that comprise antigenicdeterminants of microbial pathogens that are known to cause infection inabdominal lymph nodes.

MRV for Metastasis to the Skin and Perineum

Patient U (PtU) was diagnosed with colon cancer and was treated withexcision of the primary tumour in November year 0. He was diagnosed withstage 4 cancer in July year 2 with metastases to the perineum (i.e.,peri-anal/genital soft tissue area) and skin. He had further surgery toremove as much of the cancer as possible in the perineum (cancerextended past surgical margins) with follow-up radiation andchemotherapy. The only known cancer sites remaining were in the skin andperineum. PtU started treatment with MRV, which contains Staphylococcusaureus a common cause of skin and perineal infection, on May 25, year 3,which he continued three times per week for 5 months. In spite of hisoriginal poor prognosis, PtU is in excellent health more than 10 yearsafter his diagnosis with stage 4 cancer with metastases to the perineumand skin.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of cancer of the skin and perineum withadministration of antigenic compositions that comprise antigenicdeterminants of microbial pathogens that are known to be common causesinfection in the skin and perineum.

PVF for Metastases to the Peritoneum

Patient V (PtV) was diagnosed with breast cancer in May, year 0, atwhich time she had a mastectomy with adjuvant chemotherapy. In January,year 12, she developed abdominal pain and ascites and was diagnosed withperitoneal metastases, a diagnosis with a poor prognosis. On August 5,year 12, PtV began treatment with PVF, which contains E. coli a commoncause of peritoneal infection, which she continued regularly for 1 year.Her tumour markers and ascites decreased and, in August year 13, afterone year of PVF treatment, she had abdominal surgery for an unrelatedmedical condition, at which time the surgeon could not find any evidenceof the previous peritoneal cancer. PtV discontinued use of the vaccine.PtV was still alive at last contact, 3 years and 9 months after beingdiagnosed with terminal peritoneal metastases.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of peritoneal metastases with administration ofantigenic compositions that comprise antigenic determinants of microbialpathogens that are known to cause peritoneal infection.

PVF for Ovarian and Pelvic Cancer

Patient W (PtW) was diagnosed with stage 3B poorly differentiatedovarian cancer in the fall of year 0. She had surgery in November year0, with removal of the left ovary, but the cancer could not becompletely excised and thus, she was at extreme risk for recurrence. Shehad a full course of post-operative chemotherapy. However, in year 2 hertumour markers began to rise and in January year 3 she was diagnosedwith a recurrence in her right ovary area. She had surgery to removethis right ovarian mass in February year 3, but again the cancer couldnot be completely excised and she had follow-up chemotherapy. However,once again in December year 3 she developed a further recurrence in thepelvic area and retroperitoneal lymphadenopathy. She began treatmentwith PVF vaccine, which contains E. coli a cause of ovarian and pelvicinfection, on January 5, year 4, which she continued for 6 months. Hertumour markers, which had risen to 2600, fell to the 300 range. PtW wasalive and feeling very well at last contact, 2 years and 9 months afterbeing diagnosed with recurrent ovarian cancer. Of note is the fall inher tumour markers following PVF treatment.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of ovarian and pelvic cancer with administrationof antigenic compositions that comprise antigenic determinants ofmicrobial pathogens that are known to cause infection in the ovary andpelvic areas.

MRV for Follicular Non-Hodgkin's Lymphoma

Patient Y (PtY): was diagnosed with stage 4A Follicular Non-Hodgkin'slymphoma, with extensive marked lymphadenopathy (i.e., enlarged lymphglands). He declined all conventional treatment. PtY began treatmentwith the MRV composition, which contains many of the pathogens whichcommonly cause infection of the lymph nodes of the head and neck,axillae, mediastinum and inguinal areas. In addition, he began treatmentwith a multiple vitamin/supplement regime, healthful diet and otherimmune enhancement treatments. He continued regular use of this vaccinefor more than 3 years, at which time his lymph glands had begun togreatly reduce in size and he was feeling well. This resolution oflymphadenopathy continued, and imaging showed almost complete resolutionof previous extensive lymphadenopathy. PtY was feeling well and therewas no lymphadenopathy palpable: a clearly remarkable recovery. Fiveyears after his initial diagnosis with Stage 4A Follicular Non-Hodgkin'slymphoma, PtY had no evidence of recurrence and was leading an activeand healthy life. Treatment with MRV vaccine resulted in completeremission of his stage 4A follicular non-Hodgkins' lymphoma.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of lymphoma with administration of antigeniccompositions that comprise antigenic determinants of microbial pathogensthat are known to be common causes of lymph node infection in the regionthe lymphoma is located.

PVF for Colon Cancer with Metastases to the Liver and Kidneys

Patient Z (PtZ) was diagnosed with metastatic spread of previouslytreated colon cancer, with a metastasis to the liver and probable othermetastases to both kidneys. The liver metastasis was excised. Theprognosis for this stage (i.e., stage 4) of colon cancer is poor and thebenefit of further conventional treatment (i.e., chemotherapy) islimited. PtZ declined chemotherapy initially. Three months afterdiagnosis with metastatic colon cancer, PtZ began treatment withPolyvaccinum Forte (PVF), which contains E. coli, a common cause ofinfection of the colon, liver and kidneys. In addition PtZ begantreatment with a multiple vitamin/supplement regime and healthful diet.He continued regular use of this vaccine and the vitamin and supplementregime, and began chemotherapy. Although the overall course of hisdisease was slowly progressive, with development of lung metastases andrecurrence of liver metastases, 28 months after his initial diagnosis ofmetastatic disease, his weight was stable and his energy levels weregood. Three years (36 months) after diagnosis of stage 4 colon cancer,PtZ was feeling well except for nausea and mild weight loss related tochemotherapy.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of cancer of the colon, liver and kidneys withadministration of antigenic compositions that comprise antigenicdeterminants of microbial pathogens that are known to be pathogenic inthe colon, liver and kidneys.

PVF for Colon Cancer with Metastases to the Liver, Porta Hepatic LymphNodes and Lung

Patient AA (PtAA) was diagnosed with metastatic colon cancer withmetastases to the liver, portahepatic lymph nodes and lungs. Theprognosis for this stage (i.e., stage 4) of colon cancer is very poor(i.e., ‘terminal’ cancer) and the benefit of conventional treatment(i.e., chemotherapy) is limited. PtAA began chemotherapy, butdiscontinued treatment approximately 5 months after his diagnosis due toside effects, at which time he began treatment with Polyvaccinum Forte(containing bacterial species which cause infection in the colon, liver,abdominal lymph nodes and lungs) every second day as well as a multiplevitamin/supplement regime and a healthy diet. PtAA's subsequent CT Scansdemonstrated necrotic porta hepatic lymph nodes unchanged in size fromthe time of his diagnosis and no change in size of the lung metastases,although the two liver metastases grew moderately in size (3.4 cm to 4.5cm and 1.2 cm to 3.0 cm). In spite of the very poor prognosis, PtAAcontinued to feel quite well almost one year after a diagnosis ofterminal cancer.

In accordance with the foregoing results, one aspect of the inventioninvolves the treatment of cancer of the colon, liver, abdominal lymphnodes and lungs with administration of antigenic compositions thatcomprise antigenic determinants of microbial pathogens that are known tobe pathogenic in the colon, liver, abdominal lymph nodes and lungs.

Example 3: Microbial Pathogens

In alternative aspects, the invention utilizes microbial antigens, suchas bacterial or viral antigens, to formulate antigenic compositions,where the microbial species is selected on the basis of the tissue ororgan within which the microbe is known to cause infections. Bacterialresident flora are the most common bacterial pathogens, accounting forthe vast majority of bacterial infections in most animals, includinghumans. Resident flora can for example infect through primaryattachment, or attachment and invasion following mucosa damage,resulting for example from vascular, trauma, chemical insult, or damageresulting from primary infection.

For microbial pathogens, virulence and infection potential is acombination of the ability of the microbe to adhere, to produce enzymes,to survive immunoproducts (complement, antibody) and to survive themicrobiocidal activity of macrophage and neutrophils. Some bacteria,including endogenous bacteria, may be sufficiently virulent as to causemonomicrobial infections, while others are more effective with thesynergy of polymicrobial infection. In general, it is often not possibleto be precise about the specific role of individual microbes within themilieu of mixed infection. As acute infection may, in some cases,provide more optimal immune stimulation, accordingly, in someembodiments, the invention utilizes microbial species that are involvedin acute infection.

In some embodiments, bacteria that are members of the endogenous floraof a particular region may be used to formulate antigenic compositionsof the invention. The rows of Table 6 list a number of bacterialspecies, together with the biological regions in which each species mayform a part of the endogenous flora. For example, Abiotrophia spp. aretypically members of the endogenous flora of the respiratory tract andthe mouth. Further and for example, the organisms listed in Table 6 maybe used as microbial pathogens to formulate antigenic compositions, orantigenic compositions having those pathogens may be selected, for useto treat inflammatory conditions, cancers, for example as ananti-inflammatory treatment for cancers, inflammation associated withcancers, or inflammatory conditions situated in the tissues or organslisted with the relevant organism in Table 6.

TABLE 6 Human Bacterial Normal Flora (Endogenous Bacterial HumanPathogens) Duodenum/ GU Bacterial species Respiratory Mouth StomachJejunum Ileum Colon System Genital Skin CFU/mL 10{circumflex over ( )}510{circumflex over ( )}2 10{circumflex over ( )}5 10{circumflex over( )}8 10{circumflex over ( )}11 Abiotrophia + + spp Acholeplasma + +laidlawii Acidaminococcus + + + + + fermentansAcinetobacter + + + + + + + + spp. Actinobacillus + + spp.Actinobaculum + + + + + spp. Actinomyces + + + + + + + spp. Aerococcus +christensenii Aerococcus + viridans Aerococcus + urinae Aeromonas + + +spp. Alloiococcus + otitis Anaerorhabdus + + furcosusAnaerococcus + + + + hydrogenalis Anaerococcus + + + lactolyticusAnaerococcus + + + prevotii Arcanobacterium + + spp. Atopobium + + + + +spp. Bacillus + + + spp. Bacteroides + + caccae Bacteroides + +distasonis Bacteroides + + eggerthii Bacteroides + + + + fragilisBacteroides + + merdae Bacteroides + + ovatus Bacteroides + +splanchnicus Bacteroides + + thetaiotaomicron Bacteroides + + vulgatusBifidobacterium + + + adolescentis Bifidobacterium + + + + + bifidumBifidobacterium + + + + + breve Bifidobacterium + + + + + catenulatumBifidobacterium + + + + + + + dentium Bifidobacterium + + + + + longumBilophila + + + + + + + wadsworthia Brevibacterium + caseiBrevibacterium + epidermidis Burkholderia + + + + cepaciaButyrivibrio + + + fibrisolvens Campylobacter + + + + concisusCampylobacter + + + + curvus Campylobacter + + + + gracilisCampylobacter + + + jejuni Campylobacter + + + rectusCampylobacter + + + + + showae Campylobacter + + sputorumCapnocytophaga + + granulosum Capnocytophaga + + gingivalisCampylobacter + + haemolytica Capnocytophaga + + + + + + + ochraceaCapnocytophaga + + sputigena Cardiobacterium + + hominis Cedecea + sppCentipeda + + periodontii Citrobacter + + + freundii Citrobacter + + +koseri Clostridium + + + spp. Corynebacterium + + + accolensCorynebacterium + + + afermentans Corynebacterium + amycolatumCorynebacterium + auris Corynebacterium + + diphtheriaeCorynebacterium + durum Corynebacterium + glucuronolyticumCorynebacterium + jeikeium Corynebacterium + macginleyiCorynebacterium + matruchotii Corynebacterium + minutissimumCorynebacterium + propinquum Corynebacterium + pseudodiphtheriticumCorynebacterium + riegelii Corynebacterium + simulansCorynebacterium + + striatum Corynebacterium + ulceransCorynebacterium + + urealyticum Dermabacter + hominis Dermacoccus +nishinomiyaensis Desulfomonas + + + pigra Dysgonomonas + + + spp.Eikenella + + + + + corrodens Enterobacter + + + aerogenesEnterobacter + + + cloacae Enterobacter + + + gergoviaeEnterobacter + + + sakazakii Enterobacter + + + tayloraeEnterococcus + + + spp. Escherichia + + + + + coli Escherichia + + +fergusonii Escherichia + + + hermannii Escherichia + + + vulnerisEubacterium + + + + + spp. Ewingella + + americana Finegoldia + + + + +magnus Fusobacterium + + alocis Fusobacterium + + + + + gonidiaformansFusobacterium + + + mortiferum Fusobacterium + + + + + naviformeFusobacterium + + + + + necrophorum Fusobacterium + + + nucleatumFusobacterium + + sulci Fusobacterium + + + russii Fusobacterium + + +varium Gardnerella + + + + + vaginalis Gemella + + haemolysansGemella + + + + + morbillorum Globicatella + + spp. Granulicatella + +spp. Haemophilus + + + spp. Hafnia alvei + + + Helcococcus + kunziiHelicobacter + + + spp. Kingella + + spp. Klebsiella + + + + + spp.Kocuria + spp. Kytococcus + sedentarius Lactobacillus + + + + + + + +acidophilus Lactobacillus + + breve Lactobacillus + + + + caseiLactobacillus + + cellobiosus Lactobacillus + + + + + + + + fermentumLactobacillus + + + + reuteri Lactobacillus + + + + + + salivariusLactococcus + + spp. Leclercia + + + adecarboxylata Leminorella + + +spp. Leptotrichia + + + + buccalis Leuconostoc + + spp.Megasphaera + + + elsdenii Micrococcus + + + luteus Micrococcus + + +lylae Micromonas + + micros Mitsuokella + + + multiacidusMobiluncus + + + + curisii Mobiluncus + + + + mulieris Moellerella + + +wisconsensis Moraxella + + catarrhalis other + + + + Moraxella spp.Morganella + + + morganii Mycoplasma + + buccale Mycoplasma + fauciumMycoplasma + + + fermentans Mycoplasma + + genitalium Mycoplasma + + +hominis Mycoplasma + + lipophilum Mycoplasma + + orale Mycoplasma +penetrans Mycoplasma + + pneumoniae Mycoplasma + primatum Mycoplasma + +salivarium Mycoplasma + spermatophilum Neisseria + cinerea Neisseria +flavescens Neisseria + lactamica Neisseria + + meningitidis Neisseria +mucosa Neisseria + polysaccharea Neisseria + sicca Neisseria + subflavaOligella + + ureolytica Oligella + + urethralis Pantoea + + +agglomerans Pastuerella + + bettyae Pasteurella + + multocidaPediococcus + + spp. Peptococcus + + + niger Peptoniphilus + + + + + +asaccharolyticus Peptoniphilus + lacrimalis Peptostreptococcus + + + + +anaerobus Peptostreptococcus + + + productus Peptostreptococcus + + +vaginalis Porphyromonas + + + + + + asaccharolytica Porphyromonas + + +catoniae Porphyromonas + + + endodontalis Porphyromonas + + + gingivalisPrevotella + + bivia Prevotella + + + buccae Prevotella + + + + +buccalis Prevotella + + + corporis Prevotella + + + dentalisPrevotella + + + denticola Prevotella + + disiens Prevotella + + +enoeca Prevotella + + + heparinolytica Prevotella + + + intermediaPrevotella + + + + + loescheii Prevotella + + + + + melaninogenicaPrevotella + + + nigrescens Prevotella + + + + + oralis Prevotella + + +oris Prevotella + + + oulorum Prevotella + + + tanneraePrevotella + + + + + veroralis Prevotella + + + zoogleoformansPropionibacterium + acnes Propionibacterium + avidum Propionibacterium +granulosum Propionibacterium + + propionicum Propionfera × + innocuumProteus + + + mirabilis Proteus + + + penneri Proteus + + + vulgarisProvidencia + + rettgeri Providencia + + + stuartii Pseudomonas + + +aeruginosa Retortamonas + + + intestinalis Rothia + + dentocariosaRothia + + mucilaginosa Ruminococcus + + + productus Selenomonas + +spp. Serratia + + liquefaciens Serratia + + marcescens Serratia + +odorifera Staphylococcus + + + + + aureus Staphylococcus + auricularisStaphylococcus + capitis Staphylococcus + caprae Staphylococcus + cohniiStaphylococcus + + + + + epidermidis Staphylococcus + haemolyticusStaphylococcus + hominis Staphylococcus + lugdunensis Staphylococcus +pasteuri Staphylococcus + saccharolyticus Staphylococcus + +saprophyticus Staphylococcus + schleiferia Staphylococcus + simulansStaphylococcus + xylosus Staphylococcus + warneriStreptococcus + + + + + agalactiae Streptococcus + + + + + + + anginosusStreptococcus + + + bovis Streptococcus + + + + + + + constellatusStreptococcus + + criceti Streptococcus + + crista Streptococcus + +equisimilis Streptococcus + + gordonii Streptococcus + + + + + +intermedius Streptococcus + + + mitis Streptococcus + + mutansStreptococcus + + oralis Streptococcus + + parasanguis Streptococcus +pneumoniae Streptococcus + + + + pyogenes Streptococcus + + + salivariusStreptococcus + + + sanguis Streptococcus + + sobrinus Streptococcus + +vestibularis Group C + G + + Streptococci Succinivibrio + + +dextrinosolvens Sutterella + + + + + spp. Suttonella + + indologenesTissierella + + + praeacuta Treponema + + denticola Treponema + +maltophilum Treponema + minutum Treponema + phagedenis Treponema +refringens Treponema + + socranskii Treponema + + vincentii Turicella +otitidis Ureaplasma + + + urealyticum Veillonella + + + + + spp.Weeksella + + virosa

Endogenous microbial flora, such as bacteria, have access to tissues forpathogenesis either through contiguous spread or bacteremic spread.Under favorable conditions, all endogenous organisms can becomepathogenic and invade locally and spread by contiguous spread toadjacent tissues and organs. Endogenous bacterial flora of the skin,mouth and colon are the species that are understood to also be amenableto bacteremic spread. Bacteria that are members of a particularendogenous flora domain may therefore cause infection in tissues ororgans to which these bacteria may spread. Accordingly, one aspect ofthe invention involves the use of endogenous microbial pathogens totreat a cancer of a tissue or organ to which the endogenous bacteria mayspread to cause infection. The columns of Table 7 list 9 domains forendogenous flora, the: skin, respiratory system, genitals, GU system,mouth, stomach, duodenum/jejunum, ileum and colon. The rows of Table 7list organs or tissues within which cancers may be situated.Accordingly, one aspect of the invention involves the use of endogenousmicrobial pathogens to formulate antigenic compositions, or theselection of existing formulations having the pathogens, for treatingcancers situated in tissues or organs to which the pathogen may spreadto cause an infection. Accordingly, in alternative embodiments, tumorssituated in the tissues or organs listed in the first column of Table 7may be treated with antigenic compositions comprising antigenicdeterminants that are specific for microbial pathogens that are membersof the endogenous flora of one or more of the endogenous flora domainslisted in the first row of Table 7 and indicated with an X or a checkmark in the appropriate row. For example, tumors situated in theprostate may be treated with an antigenic composition having antigenicdeterminants specific for a microbial pathogen or pathogens endogenousto the GU system and/or genital system. A number of the bacterialspecies that are endogenous to the endogenous flora domains listed inTable 7 are listed, with the corresponding endogenous flora domains, inTable 6. Accordingly, one aspect of the invention involves the treatmentof a cancer situated in a tissue listed in Table 7 with an antigeniccomposition comprising antigenic determinants of the bacterial speciesthat are listed in Table 6, where the regions of endogenous flora linkedto the site of the tumor in Table 7 match the regions of endogenousflora linked to the bacterial species in Table 6. The examples providedin Tables 6 and 7 may be used to formulate antigenic compositions foruse in treating inflammatory conditions, cancers, for example as ananti-inflammatory treatment for cancers, inflammation associated withcancers, or inflammatory conditions situated in the organs identified inTables 6 and 7.

TABLE 7 Tissue/Organ Pathogenicity of Endogenous Flora Duo- Tissue/organGU denum/ site Skin Respiratory Genital System Mouth Stomach JejunumIleum Colon Skin x x Soft tissue x (i.e. fat and muscle) (e.g., sarcoma)Breast x x Lymph x x x nodes: head and neck Lymph x ✓ ✓ nodes:axillae/arm Lymph x ✓ ✓ nodes: mediastinal Lymph x nodes: pulmonaryhilum Lymph x ✓ x x x x nodes: intra- abdominal Lymph x X ✓ ✓ nodes:inguinal/ leg Hematological ✓ ✓ ✓ (e.g. leukemias, multiple myeloma)Bone x ✓ ✓ Joints x ✓ ✓ ✓ Meninges x x Brain ✓ ✓ ✓ Spinal cord ✓ ✓ ✓Eye/Orbit x x X x Salivary x glands Oral x Tonsil x x Nasopharynx/ x xSinus Thyroid ✓ ✓ ✓ Larynx x x Lung/Trachea/ x Bronchi Pleura ✓ x ✓ ✓Mediastinum x Heart ✓ ✓ □ Esophagus x Stomach x Small x x bowel Colon/ xRectum Anus x x Perineum x x Liver ✓ ✓ ✓ Gallbladder x Biliary tract xPancreas x Spleen ✓ ✓ ✓ Adrenal ✓ ✓ ✓ gland Kidney ✓ x ✓ ✓ Ureter xBladder ✓ x x Peritoneum x x x x Retroperitoneal x x x x x area Prostatex x Testicle x x Penis x x x Ovary/ x x x Adnexae Uterus x x x Cervix xx x Vagina x x Vulva x x *Bacteria have access to tissues/organs eitherthrough: Contiguous spread (X) or Bacteremic spread: (✓).

In accordance with the combined information in Tables 6 and 7, cancerslocated in the tissues or organs set out in column 1 of Table 7 may betreated with antigenic compositions comprising antigenic determinants ofthe corresponding bacterial species of Table 6, so that the columnheadings in Table 7 are in effect replaced with the bacterial species ofTable 6.

In some embodiments, microbial pathogens for use in the invention may beexogenous bacterial pathogens. For example, the organisms listed inTable 8 may be used as microbial pathogens to formulate antigeniccompositions, or antigenic compositions having those pathogens may beselected, for use to treat inflammatory conditions, cancers, for exampleas an anti-inflammatory treatment for cancers, inflammation associatedwith cancers, or inflammatory conditions situated in the tissues ororgans listed with the relevant organism in Table 8. In someembodiments, antigenic determinants of both endogenous and exogenousbacterial species targeted to a specific tissue or organ may be used incombination. For example, an antigenic composition derived from, orspecific for, Clostridium difficile, may be used to treat inflammatoryconditions, cancers, for example as an anti-inflammatory treatment forcancers, inflammation associated with cancers, or inflammatoryconditions situated in the colon.

TABLE 8 Exogenous Bacterial Human Pathogens, and their Sites ofInfection bacterial species tissue/organ sites Achromobacterhematological, skin, soft tissue, lung/trachea/bronchi, spp. peritoneum,meninges, bile duct, gallbladder, kidney, bladder, ureter Actinomaduraskin, soft tissue, lung/trachea/bronchi, mediastinum, brain, spp. spinalcord, hematological, meninges, joints Aerobacter spp. small bowel,colon, hematological, peritoneum Aerococcus spp. hematological, heart,bone, kidney, bladder, ureter, meninges Alcaligenes spp.lung/trachea/bronchi Anaplasma spp. meninges, hematological, liver,spleen, bone, lung/trachea/bronchi Bacillus anthracislung/trachea/bronchi, lymph nodes pulmonary hilum, mediastinum,meninges, skin, nasopharynx, tonsil, oral, small bowel, colon,hematological Bacillus cereus colon, eye, hematological other Bacillushematological, bone, meninges, brain, heart, spp. lung/trachea/bronchi,mediastinum, skin, soft tissue, colon, stomach, small bowel, eyeBalneatrix spp. lung/trachea/bronchi, meninges, hematological Bartonellaskin, hematological, liver, muscle, lymph nodes, joints bacilliformisBartonella brain, spinal cord, hematological, skin, liver, bone, pleura,henselae lung/trachea/bronchi, mediastinum, axillary and inguinal lymphnodes, eye, joints Bartonella skin, hematological, liver, spleen, jointsquintana Bergeyella skin, soft tissue, meninges, hematological,zoohelcum lung/trachea/bronchi Bordetella lung/trachea/bronchi,hematological holmesii Bordetella nasopharynx, tonsil,lung/trachea/bronchi parapertussis Bordetella nasopharynx, tonsil,lung/trachea/bronchi pertussis Borrelia meninges, brain, spinal cord,skin, eye, hematological, burgdorferi inguinal/axillary/cervical lymphnodes, muscle, liver, spleen, nasopharynx, lung/trachea/bronchi, testes,joints Borrelia brain, spinal cord, hematological, small bowel, liver,recurrentis spleen, salivary glands, lung/trachea/bronchi, lymph nodes,eye, skin Brevundimonas peritoneum, hematological, skin, soft tissuespp. Brucella spp. lung/trachea/bronchi, lymph nodes pulmonary hilum,meninges, brain, spinal cord, lymph nodes, mediastinum, bone, eye, smallbowel, colon, liver, biliary tract, kidney, ureter, bladder,hematological, skin, testes, spleen, prostate, joints Burkholderiahematological, meninges, lung/trachea/bronchi gladioli Burkholderialung/trachea/bronchi, skin, soft tissue, liver, spleen, mallei muscle,lymph nodes pulmonary hilum, mediastinal lymph nodes, mediastinum, headand neck lymph nodes, hematological Burkholderia lung/trachea/bronchi,skin, kidney, bladder, ureter, soft pseudomallei tissue, bone, brain,spinal cord, muscle, hematological, prostate, kidney, ureter, meningesCalymmatobacterium skin, penis, vulva, soft tissue, vagina, cervix,bone, granulomatis hematological, inguinal lymph nodes Campylobactersmall bowel, colon coli Campylobacter lung/trachea/bronchi, small bowel,colon, meninges, brain, fetus peritoneum, bone, gallbladder, ovaries,hematological, heart, kidney, bladder, ureter Campylobacter colon,hematological, gallbladder, pancreas, bladder, jejuni bone, meningesCampylobacter small bowel, colon sputorum Capnoctyophaga skin, softtissue, meninges, hematological, bone, canimorsus lung/trachea/bronchi,eye Capnoctyophaga skin, soft tissue, meninges, hematological, bone,cynodegmi lung/trachea/bronchi, eye CDC groups EF- hematological, eye,skin, soft tissue 4a and EF-4b Chlamydia lung/trachea/bronchi, lymphnodes pulmonary hilum, liver, pneumoniae brain, meninges, skin, thyroid,pancreas, hematological Chlamydia psittaci lung/trachea/bronchi, lymphnodes pulmonary hilum, mediastinum, liver, brain, meninges,hematological, skin, thyroid, pancreas Chlamydia inguinal lymph nodes,penis, vulva, vagina, cervix, uterus, trachomatis ovaries and adnexae,peritoneum, prostate, eye Chlamydophila laryngx, trachea/bronchi,hematological pneumoniae Chromobacterium hematological, liver, spleen,lung/trachea/bronchi, kidney, violaceum bladder, ureter, eye/orbit,bone, brain, meninges, spinal cord Chlamydophila lung/trachea/bronchipsittaci Chryseobacterium meninges, lung/trachea/bronchi, hematologicalspp. Clostridium small bowel, colon, stomach, skin, soft tissue,bifermentans hematological Clostridium colon, small bowel, skinbotulinum Clostridium colon difficile Clostridium indolis small bowel,colon, stomach, skin, soft tissue, hematological Clostridium smallbowel, colon, stomach, skin, soft tissue, mangenolii hematologicalClostridium small bowel, colon, stomach, skin, soft tissue, perfringenshematological, heart Clostridium small bowel, colon, stomach, skin, softtissue, sordellii hematological Clostridium small bowel, colon, stomach,skin, soft tissue, sporogenes hematological Clostridium small bowel,colon, stomach, skin, soft tissue, subterminale hematologicalClostridium tetani skin, soft tissue Comamonas spp. hematological,peritoneum, eye Corynebacterium neck/axillary/inguinal/mediastinal lymphnodes, lymph pseudotuberculosis nodes pulmonary hilum,lung/trachea/bronchi, mediastinum Coxiella burnetiilung/bronchi/trachea, brain, spinal cord, liver, bone, jointsEdwarsiella tarda skin, soft tissue, liver, meninges, small bowel,colon, bone, uterus, ovaries Ehrlichia spp. meninges, brain, spinalcord, hematological, bone, liver, kidney, spleen, lymph nodesErysipelothrix skin, hematological, bone, brain, peritoneumrhusiopathiae Francisella nasopharynx, oral, tonsil,lung/trachea/bronchi, skin, tularensis axillary/head and neck/inguinallymph nodes, hematological, eye, small bowel Fusobacterium skin, softtissue, hematological spp. Gordonia spp. skin, soft tissue,lung/trachea/bronchi, mediastinum, brain, spinal cord, hematological,meninges, eye Haemophilus skin, inguinal lymph nodes, penis, vulva,vagina ducreyi Helicobacter stomach pylori Legionella spp.lung/trachea/bronchi, lymph nodes pulmonary hilum, hematological, brain,spinal cord, muscle, pancreas Leptospirosis spp. lung/trachea/bronchi,pancreas, meninges, brain, spinal cord, skin, lymph nodes, eye,hematological, nasopharynx, oral, tonsil, kidney, liver, spleen Listeriahematological, brain, meninges, spinal cord, small bowel, monocytogenescolon Methylobacterium hematological, peritoneum, skin, soft tissue,bone spp. Mycobacterium lung/bronchi/trachea, lymph nodes pulmonaryhilum, avium prostate, pancreas, spleen, skin, neck lymph nodes,esophagus, bone, hematological Mycobacterium colon, small bowel, jointsbovis Mycobacterium lung/bronchi/trachea, lymph nodes pulmonary hilum,kansasii prostate, bone Mycobacterium skin, soft tissues, testes, eyeleprae Mycobacterium skin, soft tissue, bone marinum Mycobacterium headand neck lymph nodes scrofulaceum Mycobacterium lung/bronchi/trachea,lymph nodes pulmonary hilum, tuberculosis prostate, peritoneum,pancreas, spleen, lymph nodes, small bowel, meninges, brain, spinalcord, kidney, ureter, bladder, muscle, esophagus, colon, testes, eye,ovaries, cervix, vagina, uterus, mediastinum, larynx, skin,hematological, pleura, joints Mycobacterium skin, soft tissue ulceransother lung/bronchi/trachea, lymph nodes pulmonary hilum, skin,Mycobacterium soft tissues, bone, head and neck lymph nodes, joints spp.Myroides spp. kidney, bladder, ureter, skin, soft tissue, hematologicalNeisseria nasopharyx, oral, tonsil, prostate, penis, vagina, cervix,gonorrhoeae uterus, ovary/ad nexae, peritoneum, skin, muscle, bone,liver, hematological, head and neck and inguinal and intra- abdominallymph nodes, anus, joints Neorickettsia hematological, bone, lymphnodes, liver, spleen sennetsu Nocardia spp. lung/bronchi/trachea,pancreas, meninges, spinal cord, brain, skin, soft tissue, eye, bone,kidney, heart, hematological Orientia meninges, brain, spinal cord,hematological, skin, inguinal tsutsugamushi and axillary lymph nodes,spleen, lung/bronchi/trachea Pandoraea spp. lung/trachea/bronchi,hematological Pasteurella canis skin, soft tissue, hematologicalPasteurella skin, soft tissue, hematological dagmatis Pasteurella skin,soft tissue, hematological stomatis Pediococcus spp. hematological,liver, colon Pityrosporum skin ovale Plesiomonas small bowel, colon,hematological, meninges, bone, gall shigelloides bladder, skin, softtissue Pseudomonas lung/trachea/bronchi, hemaotogical, skin, softtissue, bone, aeruginosa meninges, brain, eye, kidney, bladder, ureter,heart, joints other skin, soft tissue, lung/trachea/bronchi,mediastinum, Pseudomonas hematological spp. Ralstonia spp.hematological, meninges, bone Rhizobium spp. hematological, peritoneum,eye, kidney, bladder, ureter Rhodococcus lung/trachea/bronchi,hematological, brain, skin, lymph spp. nodes, bone, mediastinum, liver,spleen, soft tissue, spinal cord, meninges Rickettsia akari skinRickettsia conorii lung/bronchi/trachea, lymph nodes pulmonary hilum,meninges, brain, spinal cord, hematolofical, skin, kidney, liver,spleen, pancreas Rickettsia felis skin, brain, spinal cord Rickettsiameninges, brain, spinal cord, hematological, prowazekiilung/bronchi/trachea, skin, spleen Rickettsia lung/bronchi/trachea,lymph nodes pulmonary hilum, rickettsiae meninges, brain, spinal cord,hematological, muscle, small bowel, liver, skin Rickettsia slovaca skin,head and neck lymph nodes Rickettsia typhi meninges, hematological,liver, kidney, brain, lung/bronchi/trachea, spleen Roseomonas spp.hematological, peritoneum, skin, soft tissue, bladder, kidney, ureterSalmonella spp. lung/bronchi/trachea, pancreas, spleen, intra-abdominallymph nodes, stomach, small bowel, colon, meninges, skin, muscle, bone,hematological, heart, joints Shewanella spp. skin, soft tissue, eye,bone, hematological, peritoneum Shigella boydii colon Shigella colondysenteriae Shigella flexneri colon Shigella sonnei colonSphingobacterium brain, meninges, spinal cord, eye, skin, soft tissuespp. Sphingomonas hematological, meninges, peritoneum, skin, softtissue, spp. kidney, bladder, ureter Spirillum minus skin,axillary/inguinal/neck lymph nodes, hematological, liver, spleen otherSpirillum colon spp. Stenotrophomonas meninges, hematological,peritoneum, maltophilia lung/trachea/bronchi, eye, kidney, bladder,ureter, skin, soft tissue Streptobacillus skin, bone, hematological,lung/trachea/bronchi, meninges, moniliformis brain, liver, spleenStreptococcus skin, hematological, soft tissue iniae Streptococcus smallbowel, nasopharynx, bone, meninges, zooepidemicus hematological, headand neck lymph nodes Streptomices spp. skin, soft tissue,lung/trachea/bronchi, mediastinum, brain, spinal cord, hematological,meninges, joints Treponema nasopharynx, tonsil, oral, meninges, brain,spinal cord, pallidum penis, vulva, vagina, anus, cervix, eye,hematological, inguinal and head and neck lymph nodes Tropheryma brain,spinal cord, hematological, small bowel, colon, whipplei heart,lung/trachea/bronchi, eye Tsukamurella skin, soft tissue,lung/trachea/bronchi, mediastinum, brain, spp. spinal cord,hematological, meninges Vibrio cholerae colon, small bowel Vibriohematological, meninges cincinnatiensis Vibrio damsela skin, soft tissueVibrio fluvialis small bowel, colon Vibrio furnissii small bowel, colonVibrio hollisae small bowel, colon, skin, soft tissue Vibriohematological metschnikovii Vibrio colon, small bowel parahaemolyticusVibrio vulnificus soft tissue, blood, skin Yersinia nasopharynx, tonsil,small bowel, intra-abdominal lymph enterocolitica nodes, colon, muscle,lung/trachea/bronchi, liver, spleen, hematological, joints Yersiniapestis lung/trachea/bronchi, lymph nodes pulmonary hilum,inguinal/axillary/neck lymph nodes, oral, tonsil, hematological, skin,joints Yersinia small bowel, colon, abdominal lymph nodes, jointspseudotuberculosis

In some embodiments, microbial pathogens for use in the invention may beviral pathogens. Table 9 provides an exemplary list of viral pathogenstogether with the tissue and organ sites for which each viral species isreportedly a pathogen. Accordingly, one aspect of the invention involvesutilizing immunogenic compositions that are specific for the namedviruses to treat an inflammatory condition, a cancer, for example as ananti-inflammatory treatment for cancers, or inflammation associated withcancers or other inflammatory condition, situated in the organs ortissues that are identified adjacent to the name of the virus in Table9. For example, an antigenic composition derived from, or specific for,a vaccinia virus, may be used to treat an inflammatory condition, acancer, for example as an anti-inflammatory treatment for cancers, orinflammation associated with cancers or other inflammatory condition,situated in the skin, hematological tissues, lymph nodes, brain, spinalcord, eye or heart.

TABLE 9 Viral Human Pathogens and Their Sites of Infection virustissue/organ sites Vaccinia skin, hematological, lymph nodes, brain,spinal cord, eye, heart Variola (smallpox) skin, hematological, lymphnodes, brain Monkeypox skin, hematological, head and neck lymph nodes,brain, eye, lung/trachea/bronchi, pulmonary hilar lymph nodes,mediastinum, nasopharynx Cowpox skin, hematological, lymph nodesParapoxviruses Skin Molluscum contagiosum skin Tanapox skin,hematological, axillary and inguinal lymph nodes Herpes Simplexnasopharynx, oral, tonsil, hematological, virus (1 and 2)lung/bronchi/trachea, pancreas, meninges, brain, spinal cord, inguinaland head/neck lymph nodes, penis, vulva, perineum, esophagus, liver,eye, skin, rectum, tonsil, mediastinum, anus, vagina, cervixVaricella-zoster nasopharynx, sinus, lung/trachea/bronchi, pulmonaryhilar lymph nodes, hematological, pancreas, meninges, brain, spinalcord, esophagus, liver, eye, skin, heart, mediastinum Cytomegalovirusnasopharynx, lymph nodes, tonsil, hematological, lung/trachea/bronchi,pancreas, abdomincal lymph nodes, brain, spinal cord, esophagus, smallbowel, colon/rectum, eye, liver, heart, skin, mediastinum, esophagusEpstein-Barr virus nasopharynx, tonsil, oral, lymph nodes,hematological, lung, abdomincal lymph nodes, brain, spinal cord,muscles, esophagus, liver, heart, skin, spleen, kidney, muscle, heart,lung/trachea/bronchi, pulmonary hilar lymph nodes, mediastinum Humanherpesvirus 6 skin, hematological, lung/trachea/bronchi, pulmonary hilarlymph nodes, brain, meninges, liver Human herpesvirus 7 skin, brain,liver Human herpesvirus 8 nasopharynx, tonsil, hematological, skin,spleen, head and neck lymph nodes Simian herpes B virus brain, spinalcord, skin, hematological, lymph nodes Adenovirus nasopharynx, oral,larynx, trachea, bronchi, lung, lymph nodes, meninges, brain, spinalcord, small bowel, colon, liver, intra-abdominal lymph nodes,mediastinum, bladder, sinus, hematological, ureter, kidney, bladder,thyroid, heart BK virus kidney Human papillomavirus skin, anus, penis,vulva, cervix, vagina, oral Hepatitis B virus liver, pancreas,hematological, bone, joints Hepatitis D virus liver Parvovirus B19 skin,hematological, nasopharynx, bone, kidney, heart, liver, brain, meninges,joints Orthoreoviruses nasopharynx, small bowel, colon, oral, sinus,lymph nodes, skin, lung/trachea/bronchi, meninges, brain, spinal cord,liver Orbiviruses brain, muscle, hematological, Coltiviruseshematological, skin, muscle, oral, spleen, lymph nodes, meninges, brainRotaviruses small bowel, colon, liver, hematological, pancreas,nasopharynx, billiary tract, meninges, brain Alphaviruses brain, spinalcord, small bowel, colon, hematological, skin, bone Rubella skin,hematological, head and neck lymph nodes, spleen, nasopharynx, bone,brain, tonsil, bronchi, liver, heart joints Yellow fever virushematological, liver, lung/trachea/bronchi, kidney, adrenal gland,spleen, lymph nodes, stomach, kidney Dengue fever virus hematological,lymph nodes, skin, spleen, muscle, liver, brain, nasopharynx, jointsJapanese encephalitis virus brain, hematological, spinal cord West Nilebrain, hematological, spinal cord, muscle, lymph nodes, encephalitisvirus liver, spleen, pancreas, meninges St. Louis brain, hematological,spinal cord, meninges, muscle, encephalitis virus nasopharynx Tick-borneencephalitis virus brain, hematological, spinal cord, muscle, meningesother Flaviviruses hematological, brain, meninges, bone, muscles, skin,lymph nodes Hepatitis C virus hematological, liver, joints Hepatitis Gvirus liver Coronaviruses nasopharynx, sinus, oral, tonsil, larynx,lung/trachea/bronchi, pulmonary hilar lymph nodes, small bowel, colon,tonsil, hematological Toroviruses small bowel, colon, hematologicalParainfluenza nasopharynx, sinus, tonsil, oral, larynx, viruseslung/trachea/bronchi, pulmonary hilar lymph nodes, meninges,hematological, mediastinum Mumps virus salivary glands, pancreas, brain,spinal cord, liver, testes, hematological, meninges, ovaries, bone,heart, kidney, thyroid, prostate, breast, joints Respiratory syncytialvirus nasopharynx, tonsil, sinus, lung/trachea/bronchi, pulmonary hilarlymph nodes, mediastinum, hematological, oral, pleura Humanmetapneumovirus nasopharynx, lung/trachea/bronchi, pulmonary hilar lymphnodes, tonsil, sinus, mediastinum, hematological, oral, pleura, larynx,eye, skin, small bowel, colon Rubeola nasopharynx, sinus, hematological,lung/trachea/bronchi, pulmonary hilar lymph nodes, intra-abdominal lymphnodes, meninges, brain, spinal cord, liver, spleen, lymph nodes, skin,thymus, eye, oral, heart Hendra virus brain, meninges,lung/trachea/bronchi, kidney, hematological, muscle, Nipah virus brain,meninges, spleen, lymph nodes, thymus, lung/trachea/bronchi, kidneys,brain, spinal cord, meninges, hematological Vesicular stomatitis virushematological, muscle, oral, tonsil, nasopharyngeal, lymph nodes, smallbowel, colon Rabies virus skin, meninges, brain, spinal cord, oral,nasopharynx, salivary glands, hematological Lyssaviruses brain, spinalcord Influenza virus nasopharynx, laryngx, lung/trachea/bronchi,pulmonary hilar lymph nodes, meninges, muscle, hematological,mediastinum, muscle, sinus, tonsil, oral, eye, pleura, brain, spinalcord, salivary glands, thyroid, heart California encephalitis virushematological, brain, meninges Hantaviruses hematological, kidney, eye,skin, oral, muscle, lung/trachea/bronchi other Bunyaviruses brain,hematological, muscle, meninges, spinal cord Lymphocyticchoriomeningitis virus hematological, muscle, lymph nodes, skin, brain,meninges, testes, bone Lassa virus nasopharynx, brain, spinal cord,lung/trachea/bronchi, pulmonary hilar lymph nodes, mediastinum, muscle,testes, eye, heart, Machupo virus brain, meninges, hematological,muscle, eye, skin, lymph nodes, nasopharynx, small bowel, colon Juninvirus brain, meninges, hematological, muscle, eye, skin, lymph nodes,nasopharynx, small bowel, colon Human T-Cell hematological, skin, lymphnodes, muscle, eye, bone, Lymphotropic viruses lung, pulmonary hilarlymph nodes, spinal cord, brain Poliovirus nasopharynx,lung/trachea/bronchi, pulmonary hilar lymph nodes, small bowel, neck andintra-abdominal lymph nodes, colon, hematological, liver, spleen, skin,brain, spinal cord, meninges, heart Coxsackieviruses nasopharynx,larynx, oral, tonsil, lung/trachea/bronchi, pulmonary hilar lymph nodes,mediastinum, pancreas, muscle, brain, meninges, small bowel, neck andintra- abdominal lymph nodes, colon, hematological, spleen, skin, eye,sinus, liver, testes, bone, pleura, salivary glands, heart Echovirusesnasopharynx, oral, tonsil, lung/trachea/bronchi, pulmonary hilar lymphnodes, muscle, brain, meninges, small bowel, neck and intra-abdominallymph nodes, colon, hematological, mediastinum, spleen, skin, eye,sinus, liver, pancreas, testes, bone, salivary glands, heart otherEnteroviruses lung/trachea/bronchi, pulmonary hilar lymph nodes,meninges, brain, skin, heart, joints Hepatitis A virus small bowel,colon, hematological, liver, spleen, brain, spinal cord, gallbladder,pancreas, kidney Rhinoviruses nasopharynx, sinus, oral, tonsil, larynx,lung/trachea/bronchi, pulmonary hilar lymph nodes Noroviruses and otherCaliciviruses small bowel, colon Astroviruses small bowel, colonPicobirnaviruses small bowel, colon Hepatitis E virus liver, smallbowel, colon, hematological

The cumulative information in Tables 6 through 9 provides an extensiveidentification of microbial pathogens that may be used in theformulation of antigenic compositions of the invention, together with anidentification of the tissues or organs in which these organisms arepathogenic, and accordingly identifies the correspondence betweenselected tissues or organs in which an inflammatory condition, cancer,or disease characterized by inflammation is situated, and the organismsthat may be used to produce antigenic formulations for treating thecondition.

In some embodiments, the microbial pathogen selected for use inantigenic compositions of the invention may be one that is a commoncause of acute infection in the tissue or organ in which the cancer tobe treated is situated. Table 10 identifies bacterial and viralpathogens of this kind, together with the tissues and organs in whichthey commonly cause infection. Accordingly, in selected embodiments, acancer residing in a tissue identified in the first column of Table 10may be treated with an antigenic composition that comprises antigenicdeterminants for one or more of the pathogenic organisms listed in thesecond column of Table 10. For example, a cancer residing in the skinmay be treated with an antigenic composition comprising antigenicdeterminants of one or more of the following organisms: Staphylococcusaureus, Beta hemolytic streptococci group A, B, C and G, Corynebacteriumdiptheriae, Corynebacterium ulcerans, Pseudomonas aeruginosa, rubeola,rubella, varicella-zoster, echoviruses, coxsackieviruses, adenovirus,vaccinia, herpes simplex, or parvo B19.

TABLE 10 Common Causes of Acute Infection (Bacterial and Viruses) ForEach Tissue/Organ Site Tissue/organ site Common Bacterial or ViralPathogens of specific tissue/organ site Skin Staphylococcus aureus, Betahemolytic streptococci group A, B, C and G, Corynebacterium diptheriae,Corynebacterium ulcerans, Pseudomonas aeruginosa rubeola, rubella,varicella-zoster, echoviruses, coxsackieviruses, adenovirus, vaccinia,herpes simplex, parvo B19 Soft tissue (i.e. Streptococcus pyogenes,Staphylococcus aureus, fat and muscle) Clostridium perfringens, otherClostridium spp. (e.g., sarcoma) influenza, coxsackieviruses BreastStaphylococcus aureus, Streptococcus pyogenes Lymph nodes:Staphylococcus aureus, Streptococcus pyogenes head and neckEpstein-Barr, cytomegalovirus, adenovirus, measles, rubella, herpessimplex, coxsackieviruses, varicella-zoster Lymph nodes: Staphylococcusaureus, Streptococcus pyogenes axillae/arm measles, rubella,Epstein-Barr, cytomegalovirus, adenovirus, varicella-zoster Lymph nodes:viridans streptococci, Peptococcus spp., mediastinal Peptostreptococcusspp., Bacteroides spp., Fusobacterium spp., Mycobacterium tuberculosismeasles, rubella, Epstein-Barr, cytomegalovirus, varicella- zoster,adenovirus Lymph nodes: Streptococcus pneumoniae, Moraxella catarrhalis,pulmonary Mycoplasma pneumoniae, Klebsiella pneumoniae, hilumHaemophilus influenza, Chlamydophila pneumoniae, Bordetella pertussis,Mycobacterium tuberculosis influenza, adenovirus, rhinovirus,coronavirus, parainfluenza, respiratory syncytial virus, humanmetapneumovirus, coxsackievirus Lymph nodes: Yersinia enterocolitica,Yersinia pseudotuberculosis, intra-abdominal Salmonella spp.,Streptococcus pyogenes, Escherichia coli, Staphylococcus aureus,Mycobacterium tuberculosis measles, rubella, Epstein-Barr,cytomegalovirus, varicella- zoster, adenovirus, influenza,coxsackieviruses Lymph nodes: Staphylococcus aureus, Streptococcuspyogenes inguinal/leg measles, rubella, Epstein-Barr, cytomegalovirus,herpes simplex Hematological Staphylococcus aureus, Streptococcuspyogenes, (e.g. leukemias, coagulase-negative staphylococci,Enterococcus spp., multiple myeloma) Escherichia coli, Klebsiella spp.,Enterobacter spp., Proteus spp., Pseudomonas aeruginosa, Bacteroidesfragilis, Streptococcus pneumoniae, group B streptococci rubeola,rubella, varicella-zoster, echoviruses, coxsackieviruses, adenovirus,Epstein-Barr, cytomegalovirus, herpes simplex Bone Staphylococcusaureus, coagulase-negative staphylococci, Streptococcus pyogenes,Streptococcus pneumoniae, Streptococcus agalactiae, other streptococcispp., Escherichia coli, Pseudomonas spp., Enterobacter spp., Proteusspp., Serratia spp. parvovirus B19, rubella, hepatitis B JointStaphylococcus aureus, coagulase-negative staphylococci, Streptococcuspyogenes, Streptococcus pneumoniae, Streptococcus agalactiae, otherstreptococci spp., Escherichia coli, Pseudomonas spp., Enterobacterspp., Proteus spp., Serratia spp., Neisseria gonorrhea, salmonellaspecies, Mycobacterim tuberculosis, Hemophilus influenza parvovirus B19,rubella, hepatitis B Scedosporium prolificans Meninges Haemophilusinfluenzae, Neisseria meningitidis, Streptococcus pneumoniae,Streptococcus agalactiae, Listeria monocytogenes echoviruses,coxsackieviruses, other enteroviruses, mumps Brain Streptococcus spp.(including S. anginosus, S. constellatus, S. intermedius),Staphylococcus aureus, Bacteroides spp., Prevotella spp., Proteus spp.,Escherichia coli, Klebsiella spp., Pseudomonas spp., Enterobacter spp.,Borrelia burgdorferi coxsackieviruses, echoviruses, poliovirus, otherenteroviruses, mumps, herpes simplex, varicella-zoster, flaviviruses,bunyaviruses Spinal cord Haemophilus influenzae, Neisseria meningitidis,Streptococcus pneumoniae, Streptococcus agalactiae, Listeriamonocytogenes, Borrelia burgdorferi coxsackieviruses, echoviruses,poliovirus, other enteroviruses, mumps, herpes simplex,varicella-zoster, flaviviruses, bunyaviruses Eye/Orbit Staphylococcusaureus, Streptococcus pyogenes, Streptococcus pneumoniae, Streptococcusmilleri, Escherichia coli, Bacillus cereus, Chlamydia trachomatis,Haemophilus influenza, Pseudomonas spp., Klebsiella spp., Treponemapallidum adenoviruses, herpes simplex, varicella-zoster, cytomegalovirusSalivary glands Staphylococcus aureus, viridans streptococci (e.g.,Streptococcus salivarius, Streptococcus sanguis, Streptococcus mutans),Peptostreptococcus spp., Bacteroides spp., and other oral anaerobesmumps, influenza, enteroviruses, rabies Oral Prevotella melaninogenicus,anaerobic streptococci, viridans streptococci, Actinomyces spp.,Peptostreptococcus spp., Bacteroides spp., and other oral anaerobesherpes simplex, coxsackieviruses, Epstein-Barr Tonsil Streptococcuspyogenes, Group C and G B-hemolytic streptococci rhinoviruses,influenza, coronavirus, adenovirus, parainfluenza, respiratory syncytialvirus, herpes simplex Sinus Streptococcus pneumoniae, Haemophilusinfluenza, Moraxella catarrhalis, α-streptococci, anaerobic bacteria(e.g., Prevotella spp.), Staphylococcus aureus rhinoviruses, influenza,adenovirus, parainfluenza Nasopharynx Streptococcus pyogenes, Group Cand G B-hemolytic streptococci rhinoviruses, influenza, coronavirus,adenovirus, parainfluenza, respiratory syncytial virus, herpes simplexThyroid Staphylococcus aureus, Streptococcus pyogenes, Streptococcuspneumoniae mumps, influenza Larynx Mycoplasma pneumoniae, Chlamydophilapneumoniae, Streptococcus pyogenes rhinovirus, influenza, parainfluenza,adenovirus, coronavirus, human metapneumovirus Trachea Mycoplasmapneumoniae parainfluenza, influenza, respiratory syncytial virus,adenovirus Bronchi Mycoplasma pneumoniae, Chlamydophila pneumoniae,Bordetella pertussis, Streptococcus pneumoniae, Haemophilus influenzaeinfluenza, adenovirus, rhinovirus, coronavirus, parainfluenza,respiratory syncytial virus, human metapneumovirus, coxsackievirus LungStreptococcus pneumoniae, Moraxella catarrhalis, Mycoplasma pneumoniae,Klebsiella pneumoniae, Haemophilus influenza influenza, adenovirus,respiratory syncytial virus, parainfluenza Pleura Staphylococcus aureus,Streptococcus pyogenes, Streptococcus pneumoniae, Haemophilusinfluenzae, Bacteroides fragilis, Prevotella spp., Fusobacteriumnucleatum, peptostreptococcus spp., Mycobacterium tuberculosisinfluenza, adenovirus, respiratory syncytial virus, parainfluenzaMediastinum viridans streptococci, Peptococcus spp., Peptostreptococcusspp., Bacteroides spp., Fusobacterium spp. measles, rubella,Epstein-Barr, cytomegalovirus Heart Streptococcus spp. (including S.mitior, S. bovis, S. sanguis, S. mutans, S. anginosus), Enterococcusspp., Staphylococcus spp., Corynebacterium diptheriae, Clostridiumperfringens, Neisseria meningitidis, Salmonella spp. enteroviruses,coxsackieviruses, echoviruses, poliovirus, adenovirus, mumps, rubeola,influenza Esophagus Actinomyces spp., Mycobacterium avium, Mycobacteriumtuberculosis, Streptococcus spp. cytomegalovirus, herpes simplex,varicella-zoster Stomach Streptococcus pyogenes, Helicobacter pyloricytomegalovirus, herpes simplex, Epstein-Barr, rotaviruses, noroviruses,adenoviruses Small bowel Escherichia coli, Clostridium difficile,Bacteroides fragilis, Bacteroides vulgatus, Bacteroidesthetaiotaomicron, Clostridium perfringens, Salmonella enteriditis,Yersinia enterocolitica, Shigella flexneri adenoviruses, astroviruses,caliciviruses, noroviruses, rotaviruses, cytomegalovirus Colon/RectumEscherichia coli, Clostridium difficile, Bacteroides fragilis,Bacteroides vulgatus, Bacteroides thetaiotaomicron, Clostridiumperfringens, Salmonella enteriditis, Yersinia enterocolitica, Shigellaflexneri adenoviruses, astroviruses, caliciviruses, noroviruses,rotaviruses, cytomegalovirus Anus Streptococcus pyogenes, Bacteroidesspp., Fusobacterium spp., anaerobic streptococci, Clostridium spp., E.coli, Enterobacter spp., Pseudomonas aeruginosa, Treponema pallidumherpes simplex Perineum Escherichia coli, Klebsiella spp., Enterococcusspp., Bacteroides spp., Fusobacterium spp., Clostridium spp.,Pseudomonas aeruginosa, anaerobic streptococci, Clostridium spp., E.coli, Enterobacter spp. herpes simplex Liver Escherichia coli,Klebsiella spp., Streptococcus (anginosus group), Enterococcus spp.,other viridans streptococci, Bacteroides spp. hepatitis A, Epstein-Barr,herpes simplex, mumps, rubella, rubeola, varicella-zoster,coxsackieviruses, adenovirus Gallbladder Escherichia coli, Klebsiellaspp., Enterobacter spp., enterococci, Bacteroides spp., Fusobacteriumspp., Clostridium spp., Salmonella enteriditis, Yersinia enterocolitica,Shigella flexneri Biliary tract Escherichia coli, Klebsiella spp.,Enterobacter spp., Enterococci spp., Bacteroides spp., Fusobacteriumspp., Clostridium spp., Salmonella enteriditis, Yersinia enterocolitica,Shigella flexneri hepatitis A, Epstein-Barr, herpes simplex, mumps,rubella, rubeola, varicella-zoster, cocsackieviruses, adenovirusPancreas Escherichia coli, Klebsiella spp., Enterococcus spp.,Pseudomonas spp., Staphylococcal spp., Mycoplasma spp., Salmonellatyphi, Leptospirosis spp., Legionella spp. mumps, coxsackievirus,hepatitis B, cytomegalovirus, herpes simplex 2, varicella-zoster SpleenStreptococcus spp., Staphylococcus spp., Salmonella spp., Pseudomonasspp., Escherichia coli, Enterococcus spp. Epstein-Barr, cytomegalovirus,adenovirus, measles, rubella, coxsackieviruses, varicella-zoster Adrenalgland Streptococcus spp., Staphylococcus spp., Salmonella spp.,Pseudomonas spp., Escherichia coli, Enterococcus spp. varicella-zosterKidney Escherichia coli, Proteus mirabilis, Proteus vulgatus,Providentia spp., Morganella spp., Enterococcus faecalis, Pseudomonasaeruginosa BK virus, mumps Ureter Escherichia coli, Proteus mirabilis,Proteus vulgatus, Providentia spp., Morganella spp., Enterococcus spp.Bladder Escherichia coli, Proteus mirabilis, Proteus vulgatus,Providentia spp., Morganella spp., Enterococcus faecalis,Corynebacterium jekeum adenovirus, cytomegalovirus PeritoneumStaphylococcus aureus, Streptococcus pyogenes, Streptococcus pneumonia,Escherichia coli, Klebsiella spp., Proteus spp., Enterococci spp.,Bacteroides fragilis, Prevotella melaninogenica, Peptococcus spp.,Peptostreptococcus spp., Fusobacterium spp., Clostridium spp.Retroperitoneal Escherichia coli, Staphylococcus aureus area ProstateEscherichia coli, Klebsiella spp., Enterobacter spp., Proteus mirabilis,Enterococci spp., Pseudomonas spp., Corynebacterium spp., Neisseriagonorrhoeae herpes simplex Testicle Escherichia coli, Klebsiellapneumoniae, Pseudomonas aeruginosa, Staphylococcus spp., Streptococcusspp., Salmonella enteriditis mumps, coxsackievirus, lymphocyticchoriomeningitis virus Penis Staphylococcus aureus, Streptococcuspyogenes, Neisseria gonorrhoeae, Treponema pallidum herpes simplex,human papillomavirus Ovary/Adnexae Neisseria gonorrhoeae, Chlamydiatrachomatis, Gardenerella vaginalis, Prevotella spp., Bacteroides spp.,Peptococcus spp. Streptococcus spp., Escherichia coli Uterus Neisseriagonorrhoeae, Chlamydia trachomatis, Gardenerella vaginalis, Prevotellaspp., Bacteroides spp., Peptococcus spp., Streptococcus spp.,Escherichia coli Cervix Neisseria gonorrhoeae, Chlamydia trachomatis,Treponema pallidum herpes simplex Vagina Gardenerella vaginalis,Prevotella spp., Bacteroides spp., peptococci spp., Escherichia coli,Neisseria gonorrhoeae, Chlamydia Trachomatis, Treponema pallidum, herpessimplex Vulva Staphylococcus aureus, Streptococcus pyogenes, Treponemapallidum herpes simplex

In selected embodiments, particular microbial pathogens are suited fortreatment of particular inflammatory conditions, including cancers, forexample as an anti-inflammatory treatment for cancers, or inflammationassociated with cancers or other inflammatory condition, located in thetissue or organ within which the organism is pathogenic, examples ofselected embodiments are set out in Table 10. These are exemplaryembodiments, and not an exhaustive list of the alternative formulationsfor use in accordance with the invention.

The specific microbes which commonly cause infection in a specifictissue or organ may vary by geographical location. For example,Mycobacterium tuberculosis is a more common cause of lung infection insome geographical locations and populations than in others andtherefore, while M. tuberculosis may not be a common lung pathogen insome geographic and population groups it may be a common lung pathogenin others. Table 10 is thus not an exhaustive list of common pathogensfor all geographic locations and population groups. It is understoodthat a clinical microbiologist skilled in the art could determine thecommon pathogenic species in a particular geographic area or populationgroup for a specific tissue or organ site in accordance with theinvention. For veterinary use, there will of course be specificpathogens that are common in selected tissues of selected species, andthis may also vary geographically.

In selected embodiments, the invention involves diagnostic steps toassess a patient's previous exposure to microbial pathogens. Forexample, the diagnostic steps may include taking a medical history ofexposure to selected pathogens, and/or evaluating a patient's immuneresponse to a selected pathogen. For example, a serology test may beconducted to detect antibodies to selected pathogens in a patient'ssera. In connection with this aspect of the invention, antigenicdeterminants of a selected microbial pathogen may be chosen for use inan immunogenic composition on a selected patient based on a diagnosticindication that the patient has had one or more prior exposure(s) to thepathogen, for example by virtue of the presence of antibodies toantigenic determinants of that pathogen in the patient's sera.

In further selected embodiments, the invention involves diagnostic stepsto assess a patient's immunological response to treatment with aselected immunogenic composition. For example, the diagnostic steps mayinclude evaluating a patient's immune response to the antigenicdeterminants of that immunogenic composition, for example using aserological test to detect antibodies to those antigenic determinants.In connection with this aspect of the invention a treatment with aselected immunogenic composition may be continued if the evaluationindicates that there is an active immunological response to theantigenic determinants of that composition, and the vaccine treatmentmay be discontinued, and an alternative treatment with a differentimmunogenic composition may be initiated, if the evaluation indicatesthat there is not a sufficiently active immunological response to theantigenic determinants of the immunogenic composition.

As discussed in the context of Patient R, in selected embodiments, themicrobial pathogen selected for use in antigenic compositions of theinvention may be one that is the most common cause of acute infection inthe tissue or organ in which the cancer to be treated is situated, whichmay provide particular benefit as illustrated by the case of Patient R.For example, for the treatment of bone cancer, Staphylococcus aureuswould be the bacterial species selected; for the treatment of cancer inlung tissue, Streptococcus pneumoniae would be selected; for thetreatment of breast cancer, Staphylococcus aureus would be selected; forthe treatment of kidney or bladder cancer, Escherichia coli would beselected; and for the treatment of colon cancer, Escherichia coli wouldbe the bacterial species selected. It is understood that a clinicalmicrobiologist skilled in the art could determine the most frequentlypathogenic species, bacterial or viral, for each specific tissue ororgan in accordance with the invention. In selected embodiments, onlyantigenic determinants of the most common pathogen for the particulartissue or organ could be used to treat cancers of that tissue or organ.In alternative embodiments, antigenic determinants of the most commonpathogen for the particular tissue or organ could be used in combinationwith antigenic determinants of other pathogens that are known to bepathogenic in the of that particular tissue or organ, preferentiallyselecting from the more common pathogens.

In some embodiments, the invention provides antigenic compositions inwhich a threshold proportion of antigenic determinants selected inaccordance with the invention are used, relative to any other antigenicdeterminants in the composition. For example, antigenic compositions mayhave greater than X % of the antigenic determinants therein derived frompathogenic (or commonly pathogenic, or most commonly pathogenic)species, where X may for example be 10, 30, 40, 50, 60, 70, 80, 90, 95or 100 (or any integer value between 10 and 100). For example, at leastX % of the antigenic determinants in the antigenic composition may bespecific for microbial pathogens that are pathogenic (or commonlypathogenic or most commonly pathogenic) in the specific organ or tissueof the patient within which the cancer is situated. Using an alternativemeasure, of the total number of microbial pathogens in the antigeniccomposition, at least X % may be selected to be microbial pathogens thatare pathogenic (or commonly pathogenic or most commonly pathogenic) inthe specific organ or tissue of the patient within which the cancer issituated. In some embodiments, the antigenic composition may accordinglyconsist essentially of antigenic determinants of one or more microbialpathogens that are each pathogenic (or commonly pathogenic or mostcommonly pathogenic) in the specific organ or tissue of the patientwithin which the cancer is situated. The following data illustrates thesurprising effectiveness of these selected formulations:

(1) The use of MRV (which contains many common respiratory tractpathogens and Staphylococcus aureus, the most common pathogen of bothbreast and bone) was found to be helpful for the treatment of breastcancer with metastases to the bone (see FIG. 6). However, survivalbenefit (survival of patients who were treated with MRV compared tothose who were not) was modest (i.e., median survival of 31 months forpatients treated with the vaccine compared to 26 months for patients nottreated with the vaccine). On the other hand, the one patient (PatientR) who was treated with a vaccine specifically targeted for breastcancer and bone cancer (i.e., containing only Staphylococcus aureus, byfar the most common cause of both breast and bone infection) had aremarkable survival benefit, surviving for more than 17 years. Theinclusion, in MRV, of other bacterial species that do not (or far lesscommonly) cause bone infection and commonly cause infection elsewhere(i.e., respiratory tract) appears to substantially reduce the benefit ofthis vaccine for the treatment of cancer of the breast and bone.(2) The survival of stage 3B lung cancer patients treated with Respivax™(i.e., median survival of 38 months and 40% 5-year survival) wassubstantially greater than the survival of stage 3B lung cancer patientstreated with MRV (i.e., median survival of 18 months and 14% 5-yearsurvival). Respivax™ contains substantially greater relativeconcentrations of the bacterial species that commonly cause lunginfection than MRV does. 67% of the bacterial cell count of Respivax™ iscomprised of bacterial species that are the common causes of lunginfection, whereas only 30% of the bacterial cell count of MRV iscomprised of bacterial species that are the common causes of lunginfection. Thus, the composition having the greater proportion ofbacteria that most commonly cause lung infections, Respivax™, is shownto be more effective for the treatment of lung cancer than the MRVformulation.(3) The survival of stage 4 colon cancer patients treated with MRV(which does not contain any colon pathogens) was poorer than patientsnot treated with a vaccine. This indicates that treatments that useantigenic determinants that are not derived from microbes that arepathogenic in the organ or tissue in which the cancer is situated maynot only be ineffective, but may also be deleterious.(4) The Murine Studies set out below, and in particular the cancer cellmodel data involving treatment with Klebsiella pneumoniae antigenicdeterminants alone, compared to treatment with Klebsiella pneumoniaeantigens in conjunction with additional antigens.The data herein accordingly provide evidence of an increasing gradationof benefit from pathogenic, to commonly pathogenic, to most commonlypathogenic for the treatment cancer within a specific organ or tissueusing targeting antigenic compositions that are derived from microbialpathogens that are pathogenic to that specific organ or tissue.

In some embodiments, the invention comprises the use of bacterial orviral vaccines that are approved for other purposes (e.g., poliomyelitisvaccine, H. influenza vaccine, meningococcal vaccine, pneumococcalvaccine, influenza vaccine, hepatitis B vaccine, hepatitis A vaccine,diphtheria vaccine, tetanus vaccine, pertussis vaccine, measles vaccine,mumps vaccine, rubella vaccine, varicella vaccine, BCG vaccine, choleravaccine, Japanese encephalitis vaccine, rabies vaccine, typhoid vaccine,yellow fever vaccine, small pox vaccine, etc.) for use as cancertreatments by selecting a vaccine containing a pathogen (or antigenicconstituent of a pathogen) that is pathogenic in the specific organ ortissue of the patient within which the cancer is situated by consultingTables 6-10. For example, a S. pneumoniae vaccine, either a whole cellvaccine or a vaccine comprised of one or more antigenic components of S.pneumoniae (e.g., pneumococcal polysaccharide-23-valent) could be usedto treat cancer at any of the following sites in which S. pneumoniae islisted as a common pathogen in Table 10: pulmonary hilar lymph nodes,hematological cancers, bone, meninges, spinal cord, eye/orbit, sinus,thyroid, bronchi, lungs, pleura or peritoneum. As a further example, ahepatitis B vaccine could be used to treat cancer at any of thefollowing sites in which hepatitis B virus is listed as a pathogen inTable 9, as follows: liver, pancreas, or hematological cancers.

In some embodiments, selected compositions and methods are specificallyexcluded from the scope of the invention. For example, the use of thefollowing microbial pathogens in the treatment of the following cancersis excluded from some embodiments, so that the claimed invention mayextend to particular embodiments with the exception of one or more ofthe following:

a) BCG (Mycobacterium bovis) for the treatment of stomach cancer andcolon cancer, for example by injection;b) Mycobacterium w for the treatment of lung cancer, for example byinjection;c) Mycobacterium vaccae for the treatment of non-small-cell lung cancer,for example by injection;d) Corynebacterium parvum for the treatment of melanoma, for example byinjection;e) Streptococcus pyogenes for the treatment of stomach cancer, forexample by injection;f) Nocardia rubra for the treatment of lung cancer or acute myelogenousleukemia, for example by injection;g) Lactobacillus casei for the treatment of cervical cancer, for exampleby injection;h) Pseudomonas aeruginosa for the treatment of lymphoma and lung cancer,for example by injection;i) Vaccinia for the treatment of melanoma, for example by injection;j) Rabies virus for the treatment of melanoma, for example by injection;k) A composition consisting of the combined antigens of the followingbacterial species for the veterinary (or, alternatively, human)treatment, for example by oral administration, for primary (or,alternatively, metastatic) cancers situated in the lung: Streptococcuspneumoniae; Neisseria catarrhalis; Streptococcus pyogenes; Haemophilusinfluenzae; Staphylococcus aureus; Klebsiella pneumoniae.l) A composition consisting of the combined antigens of the followingbacterial species for the veterinary (or, alternatively, human)treatment, for example by oral administration, for primary (or,alternatively, metastatic) cancers situated in the lung: Streptococcuspneumoniae; Neisseria catarrhalis; Streptococcus pyogenes; Haemophilusinfluenzae; Staphylococcus aureus; Klebsiella pneumoniae; Klebsiellaozaenae; Streptococcus viridans.

Example 4: Murine Studies

In the following murine studies, the following common materials wereutilized: PBS (Gibco), and mice were 7 week-old female C57BL/6.

Example 4A: Cancer of the Lung

This section relates to a Lewis lung carcinoma mouse model. Thebacterial vaccines used in this experiment were as follows:Streptococcus pneumoniae [cells and broth] vaccine (lot # J049-1[2×10⁹]; Klebsiella pneumoniae [cells and broth] vaccine (lot # J046-1[2×10⁹]; Staphylococcus aureus [cells and broth] vaccine (lot # J041-2[10×10⁹]; Escherichia coli (colon isolate) [cells and broth] vaccine(lot # J047-1 [6×10⁹]; Salmonella enterica [cells and broth] vaccine(lot # J31 [15×10⁹]; Klebsiella pneumoniae [cells only] vaccine (lot #J048-1 [2×10⁹]; and media only (Klebsiella pneumoniae media) (lot #J046-1). Mice were treated in accordance with the experimental groupingsdefined in Table 11.

TABLE 11 Experimental Groupings for Lung Cancer Mouse Model Lewis Lungi.v. s.c. injection dose schedule 10e5 cells/100 μl Day: −10, −8, −6,−4, −2, +2, +4, Group Mice Day 0 Vial # Vaccine +6, +8, +10, +12, +14,+16, etc. 1AB 8 ↓ 1 S. pneumoniae [cells 200 × 10e6 and broth] CFUs/150μl/mouse 2AB 8 2 K. pneumoniae [cells 150 × 10e6 and broth] CFUs/75μl/mouse 3AB 8 3 S. aureus [cells and 1 × 10e9 broth] CFUs/100 μl/mouse4AB 8 4 E. coli (colon) [cells 0.9 × 10e9 and broth] CFUs/150 μl/mouse5AB 8 5 S. enterica [cells and 1.5 × 10e9 broth] CFUs/100 μl/mouse 6AB 81 + 2 S. + K. pneumoniae S. 200 × 10e6 [cells and broth]* CFUs/75μl/mouse K. 150 × 10e6 CFUs/75 μl/mouse 7AB 8 8 K. pneumoniae [cells 150× 10e6 only] CFUs/75 μl/mouse 8ABC 12 9 Media only (K. pneumoniae 75μl/mouse media) (control) 9AB 8 PBS only none none

Specifically, groups of mice were pre-treated sub-cutaneously withbacterial vaccines on days −10, −8, −6, −4, and −2. On day 0, mice werechallenged intravenously with a dosage of 10e5 Lewis lung carcinomacells (Cedarlane lot #508714). Thereafter, the mice were treatedsub-cutaneously with vaccine injections every second day for theduration of the experiment as defined in Table 11. A control group wastreated with media only. Animal weights were measured and recorded every4 days. When mice started showing morbidity the experiment wasterminated. Thereafter, all mice were humanely sacrificed and the lungswere surgically removed and weighed. Lungs were placed into the vialswith Buoin's fluid and the numbers of lung nodules in each group werecounted. These results are illustrated in Table 12. Representativeexamples of these lungs are depicted in FIG. 14.

TABLE 12 Number of visible lung tumours in mice in each group Number ofvisible Group Vaccine lung tumours Average Median 1 S. pneumoniae 13, 1,7, 1, 20, 38, 50, 35 20.6 16.5 2 K. pneumoniae 1, 10, 0, 0, 1, 2, 50 9.11 3 S. aureus 1, 5, 3, 15, 10, 57, 43, 38 21.5 12.5 4 E. coli 4, 3, 0,9, 16, 3, 42, 40 14.6 6.5 5 S. enterica 0, 0, 2, 5, 2, 57, 52 16.8 2 6S + 1, 6, 0, 0, 8, 5, 47, 48 14.3 5.5 K. pneumoniae 7 K. pneumoniae 0,3, 0, 0, 0, 1, 46, 49 12.3 0.5 (cells only) 8 Control (medium) 2, 3, 12,25, 39, 26, 31.7 26 62, 39, 78

The weights of the lungs of mice injected with tumour cells were thencompared to the weights of the lungs of mice injected with PBS only, todetermine the tumour burden and thus, the therapeutic effect of vaccinetreatment. These results are illustrated in Table 13.

TABLE 13 Average lung weight (mg) and tumour weight inhibition (comparedto control) in mice immunized with killed bacterial vaccines inintravenously implanted Lewis lung carcinoma model Av. Lung Differencefrom Tumour Weight Group Vaccine weight (mg) healthy mice Inhibition (%)1 S. pneumonia (cells and 495 318 30 broth) 2 K. pneumonia (cells and298 121 73 broth) 3 S. aureus (cells and broth) 485 308 32 4 E. coli(cells and broth) 372 195 57 5 S. enterica (cells and broth) 331 154 666 S + K. pneumonia (cells and 374 197 57 broth) 7 K. pneumoniae (cellsonly) 294 117 74 8 Control (media only) 633 456 — 9 Healthy mice 177 —

Example 4B: Cancer of the Skin

This section relates to a mouse model of skin cancer. The bacterialvaccines used in this experiment were as follows: Streptococcuspneumoniae [cells and broth] vaccine (lot # J049-1 [2'10⁹]; Klebsiellapneumoniae [cells and broth] vaccine (lot # J046-1 [2×10⁹];Staphylococcus aureus [cells and broth] vaccine (lot # J041-2 [10×10⁹];Escherichia coli (colon isolate) [cells and broth] vaccine (lot # J047-1[6×10⁹]; Salmonella enterica [cells and broth] vaccine (lot # J31[15×10⁹]; Staphylococcus aureus [cells only] vaccine (lot # J041-2[10×10⁹]; and media only (S. aureus media) (lot # J041-1). Mice weretreated in accordance with the experimental groupings defined in Table14.

TABLE 14 Experimental Groupings for Skin Cancer Mouse Model B16 melanomas.c. 2 × 10e5cells/ s.c. injection dose schedule 0.1 mL Day: −10, −8,−6, −4, −2, +2, +4, Group Mice Day 0 Vaccine +6, +8, +10, +12, +14, +16,etc. AB1 8 ↓ S. pneumoniae [cells and 300 × 10e6 broth] CFUs/150μl/mouse AB2 8 K. pneumoniae [cells and 150 × 10e6 broth] CFUs/75μl/mouse AB3 8 S. aureus [cells and broth] 1 × 10e9 CFUs/100 μl/ mouseAB4 8 E. coli (colon) [cells and 0.9 × 10e9 CFUs/150 μl/ broth] mouseAB5 8 S. enterica [cells and 1.5 × 10e9 CFUs/100 μl/ broth] mouse AB6 8S. aureus [cells only] 1 × 10e9 CFUs/100 μl/ mouse ABC7 12 Media only(S. aureus 100 μl/mouse media) (control)

Specifically, groups of mice were pre-treated sub-cutaneously withbacterial vaccines on days −10, −8, −6, −4, and −2. On day 0, mice werechallenged intravenously with a dosage of 2×10e6 of B16 melanoma cells(lot #3995448; ATCC CRL-6323). Thereafter, the mice were treatedsub-cutaneously with vaccine injections every second day for theduration of the experiment as defined in Table 14. A control group wastreated with media only. Animal weights were measured and recorded every4 days. Once tumours were palpable, the tumour diameters were measuredevery second day using callipers. When mice started showing morbidity,or tumour diameters reached 20 mm in any group, the experiment wasterminated. Thereafter, all mice were humanely sacrificed. The averagevolumes of the tumours present in the groups of mice described hereinare illustrated in FIG. 15.

Example 4C: Cancer of the Colon

This section relates to a mouse model of colon cancer. The bacterialvaccines used in this experiment were as follows: Streptococcuspneumoniae [cells and broth] vaccine (lot # J049-1 [2×10⁹]; Klebsiellapneumoniae [cells and broth] vaccine (lot # J046-1 [2×10⁹];Staphylococcus aureus [cells and broth] vaccine (lot # J041-2 [10×10⁹];Escherichia coli (colon isolate) [cells and broth] vaccine (lot # J047-1[6×10⁹]; Escherichia coli (prostate isolate) [cells and broth] vaccine(lot # J040-2 [6×10⁹]; Salmonella enterica [cells and broth] vaccine(lot # J31 [15×10⁹]; and media only (E. coli media) (lot # J040-1). Micewere treated in accordance with the experimental groupings defined inTable 15.

TABLE 15 Experimental Groupings for Colon Cancer Mouse Model MC-38 coloni.p. s.c. injection dose schedule 2 × 10e5 Day: −10, −8, −6, −4, −2, +2,+4, Group Mice Day 0 Vaccine +6, +8, +10, +12, +14, +16, etc. 1AB 8 ↓ S.pneumoniae [cells 300 × 10e6 and broth] CFUs/150 μl/mouse 2AB 8 K.pneumoniae [cells 150 × 10e6 and broth] CFUs/75 μl/mouse 3AB 8 S. aureus[cells and 1 × 10e9 CFUs/100 μl/mouse broth] 4AB 8 E. coli (colon)[cells and 0.9 × 10e9 broth] CFUs/150 μl/mouse 5AB 8 E. coli (prostate)[cells 0.9 × 10e9 and broth] CFUs/150 μl/mouse 6AB 8 S. enterica [cellsand 1.5 × 10e9 broth] CFUs/100 μl/mouse 7ABC 12 Media only (E. coli 150μl/mouse media) (control)

Specifically, groups of mice were pre-treated sub-cutaneously withbacterial vaccines on days −10, −8, −6, −4, and −2. On day 0, mice werechallenged intraperitoneally with a dosage of 2×10e5 MC-38 colloadenocarcinoma cells (gift from Dr. Jeff Schlom Lab, NCI). Thereafter,the mice were treated sub-cutaneously with vaccine injections everysecond day for the duration of the experiment as defined in Table 15. Acontrol group was treated with media only. The mice were observed forthe following clinical factors: weight, cold to touch, diarrhea, rapidrespiration, closed eyes, decreased movement, piloerection, andconvulsions. When a mouse started to show signs of clinical morbidity,the mouse was humanely sacrificed and that day was defined as the day ofdeath. Survival data for this Example is depicted in FIG. 16.

Further, the health versus morbidity/mortality of the mice involved inthis Example was calculated on day 29 of the experiment as defined inTable 16.

TABLE 16 Health v. Morbidity/Mortality Group Score** Group Health StatusDay 29 Vaccine Group Score 1 7 dead; 1 tumour + ascites S. pneumoniae 22 5 dead; 1 tumour + ascites; 1 K. pneumoniae 17 tumour only; 1 healthy3 4 dead; 2 tumour + ascites; 2 S. aureus 14 tumour only 4 3 dead; 3tumour only; E. coli (colon 35 2 healthy infection isolate) 5 3 dead; 3tumour only; E. coli (prostate 35 2 healthy infection isolate) 6 3 dead;5 healthy S. enterica 50 7 12 dead Control 0 (media only) **healthy = 10points; tumour only = 5 points; tumour + ascites = 2 points; and dead =0 points.

TABLE 17 Summary of survival for each mouse group from colon cancerexperiments Mice/ MST* Vaccine group (Days) ILS** (%) # Cured P value***S. pneumoniae 8 27 12 0 0.29 K. pneumoniae 8 36 50 3 0.061 S. aureus 830 25 2 0.002 E. coli (colon) 8 35 46 3 0.008 E. coli 8 >78 >100 4 0.001(prostate) S. enterica 8 >78 >100 5 0.003 Control 12 24 0 0 —*MST—Median survival time **ILS—Increase in life span over control group***comparison to placebo treated control group Overall ComparisonSurvival: Log Rank (Mantel Cox) p = 0.001 Breslow (Generalized Wilcoxon)p = 0.003 Tarone-Ware p = 0.002

Example 4 Summary Skin Model:

There is a marked therapeutic advantage for the group treated with Staphaureus (cells-only). This study demonstrates the effectiveness of akilled S. aureus vaccine for the treatment of skin cancer in a mousemodel, consistent with the fact that S. aureus is the most common causeof skin infection in mice. The data are consistent with the use ofimmunogenic compositions of the invention to slow or inhibit cancergrowth. The S. aureus cells-only vaccine (in which media and exotoxinswere removed by centrifuging the cells and broth to collect only thecells and then reconstituting with normal saline) was more effectivethan S. aureus cells and broth vaccine (which contains media andexotoxins). This may be because S. aureus extoxins inhibit immunefunction, such as leuocidins that can kill white blood cells. Theinvention accordingly includes embodiments in which antigenicdeterminants that are to be used in immunogenic compositions areseparated from immunomodulatory compounds produced by a microbialpathogen of interest.

Lung Model:

The data presented in this Example indicate that there was substantialtumour inhibition with the immunogenic composition derived from K.pneumoniae, consistent with the fact that K. pnuemoniae is a commoncause of lung infection in mice. In mice (but generally not in humans),S. enterica can cause pneumonia, which is consistent with the beneficialeffect of this vaccine in the mouse lung model. Unlike humans, for whomS. pneumoniae is a common lung pathogen, S. pneumoniae is relativelyrarely a lung pathogen in mice (although S. pneumoniae pneumonia can beinduced in mice). E. coli and S. aureus can uncommonly cause lunginfection in mice, which is consistent with their mild benefitillustrated herein. This Example demonstrates that killed K. pneumoniaevaccine is remarkably effective for the treatment of cancer of the lungsin mice, particularly embodiments in which the immunogenic compositionincludes antigens of only the most commonly pathogenic organism (seeGroup 2 vs. Group 6).

Colon Model:

S. enterica is one of the most common causes of gastrointestinal andintraperitoneal infection in mice, which is consistent with thebeneficial effect illustrated herein in the treatment ofgastrointestinal and intraperitoneal cancer in mice.

Of the immunogenic compositions used in this Example (i.e., S. enterica,E. coli, S. aureus, K. pneumoniae, S. pneumoniae), S. enterica is themost common g.i./abdominal pathogen in mice. E. coli is the next mostcommon g.i./abdominal pathogen in mice. S. aureus and K. pneumoniae canbe found as part of the colonic flora and can cause g.i./abdominalinfection, although far less commonly. S. pneumoniae does not causeg.i./abdominal infection. In accordance with this, the S. entericavaccine is shown to be substantially beneficial in this mouse colontumour model, E. coli vaccine is shown to be moderately beneficial, S.aureus and K. pneumoniae vaccines are shown to be mildly beneficial andS. pneumoniae vaccine is shown to be of no benefit. In humans,Salmonella species cause g.i. infection and therefore, one would expectS. enterica and other Salmonella vaccines to be helpful for thetreatment of colon cancer in humans.

Example 5: Animal Models Example 5A: Illustrating the Influence of aHeat Inactivated Klebsiella pneumoniae Antigenic Composition onMonocyte/Macrophage and Dendritic Cell Populations in Mice

The following methods and materials were utilized in this Example:

Mice.

C57BL/6 female mice 7-8 weeks of age were ordered from Harlan Labs(Livermore, Calif.) for these studies.

Antibodies and Reagents.

The following antibodies were used in this Example: anti-I-A/I-E FITC(MHC Class II; M5/114.15.2); anti-Gr-1 PE (RB6-8C5); anti-CD11bPerCP-Cy5 (M1/70); anti-CD11c APC (N418); anti-CD4 FITC (GK1.5);anti-NK1.1 PE (PK136); anti-CD8a eFluor780 (53-6.7); anti-CD44 APC(IM7). All antibodies were acquired from eBioscience (San Diego,Calif.). Liberase TM and DNAse I was acquired from Roche. All media wasfrom HyClone (Fisher).

Treatment with Antigenic Compositions.

Heat killed K. pneumoniae with phenol (KO12 [5.0 OD600 units]) wasdiluted 1/10 in PBS containing 0.4% phenol and 100 μl was injectedsubcutaneously on day 0, 2, 4, and 6 into 4 mice. Control mice (n=5)were injected on day 0, 2, 4, and 6 with PBS.

Brochoalveolar Lavage.

On day 7 mice were sacrificed and a bronchoalveolar lavage (BAL) wasperformed by exposing the trachea followed by insertion of a 22Gcatheter attached to a 1 ml syringe. 1 ml of PBS was injected into thelungs and removed and placed into a 1.5 ml microcentrifuge tube. Thelungs were subsequently washed 3 more times with 1 ml of PBS and thefluid was pooled. The first wash from each mouse was centrifuged at400×g and the supernatant was frozen for cytokine analysis. The final 3ml of lavage fluid was centrifuged and the cells were pooled with thecell pellet from the first lavage. The cells were counted and stainedwith antibodies specific for MHC class II, Ly6G/C, CD11b, and CD11c.After staining the cells were washed and analyzed on a FACS Calibur flowcytometer.

Lung Digestion.

After BAL was performed the lungs were placed in 5 ml of RPMI containing417.5 μg/ml Liberase TL (Roche) and 200 μg/ml DNAse I (Roche). The lungswere then digested at 37° C. for 30 mins. After digestion the lungs wereforced through a 70 um cell strainer to create a single cell suspension.The cells were then centrifuged, washed, resuspended in FACS Buffer (PBSwith 2% FCS and 5 mM EDTA) and counted. After counting the cells werestained and analyzed by FACS using the same antibodies as for the BALcells.

Peritoneal Lavage.

1 ml of PBS was injected into the peritoneum of mice using a 1 mlsyringe attached to a 25G needle after BAL. The abdomen was massaged for1 minute and 0.5 ml of PBS was recovered from the peritoneum using a 1ml pipet. The lavage fluid was put in a 1.5 ml centrifuge tube,centrifuged at 400×g for 5 mins, and resuspended in FACS buffer prior tostaining and FACS analysis.

Spleen and Lymph Node Analysis.

The spleen and draining lymph node were removed after BAL and peritoneallavage and placed in PBS. The spleen was disrupted by mashing through a70 μm cell strainer (Fisher) and the lymph node was disrupted using therubber end of the plunger from a 1 ml syringe. After disruption, thesingle cell suspension from the spleen and lymph nodes was centrifuged,washed once with FACS Buffer, and resuspended in FACS Buffer prior tocounting, staining, and FACS analysis.

FACS Analysis.

Cells were stained on ice for 20 mins in 96 well plates using 50 ul ofantibodies diluted in FACS buffer. After 20 mins, 100 μl of FACs bufferwas added to the wells and the plates were centrifuged at 400×g for 5mins. Subsequently the media was removed and the cells were washed 1more time with FACS buffer. After the final wash the cells wereresuspended in 200 μl of FACS buffer and the data was acquired using aFACS Calibur flow cytometer (BD). A minimum of 20,000 live events werecollected for all samples except the BAL where a minimum of 5,000 eventswas collected.

The following results were obtained in this Example.

Normal mice without tumours were treated with a K. pneumoniae antigeniccomposition on day 0, 2, 4, and 6. On day 7 the mice were sacrificed andthe bronchoalveolar lavage fluid, lung tissue, peritoneal lavage fluid,lymph nodes, and spleen was analyzed for changes in monocyte andmacrophages. An increase in the number of acute inflammatory bloodmonocytes/macrophages, defined by high expression of CD11 b and Gr-1(same marker as Ly6c), and F4/80 in the lymph node draining the site ofinjection of the K. pneumoniae antigenic composition was observed (see:FIG. 17A). These acute inflammatory monocytes/macrophages also expressvery high levels of MHC class II molecules suggesting exposure tobacterial antigens. Importantly, treatment of mice with the K.pneumoniae antigenic composition for one week led to a marked increasein the frequency of acute inflammatory monocytes in the bronchoalveolarlavage fluid and in the lungs (i.e., the targeted organ) but not in thespleen or peritoneum of treated mice, suggesting that treatment caninduce homing of monocytes specifically to the lungs without affectingother organs (see: FIG. 17B). Monocytes can differentiate into dendriticcells (DCs) in the lungs and consistent with our observations of amarked increase in monocyte recruitment it was also observed that therewas a marked increase in the frequency of cells displaying markers formature DCs (see: FIG. 17C).

As illustrated in FIG. 17, treatment with a K. pneumoniae antigeniccomposition for 7 days resulted in a marked increase (compared totreatment with placebo—PBS) in both acute inflammatory monocytes anddendritic cells in the lungs of mice. As illustrated in FIG. 17, micewere treated with either a K. pneumoniae antigenic composition for orPBS on day 0, 2, 4, and 6. On day 7, the mice were sacrificed and thetotal number of A) and B) inflammatory monocytes (CD11 b+Gr-1+ cells)and C) dendritic cells (CD11c+ MHC class II+ cells) were determined byflow cytometry in the lung and spleen. The error bars depicted in A)represent the mean of 4-5 mice per group.

Example 5B. Illustrating the Influence of a Heat Inactivated Klebsiellapneumoniae Antigenic Composition and a Heat Inactivated E. coliAntigenic Composition on Monocyte/Macrophage, Dendritic Cell, andEffector Cell Populations in Mice

The following methods and materials were utilized in this Example:

Mice.

C57BL/6 female mice 7-8 weeks of age were ordered from Harlan Labs(Livermore, Calif.) for these studies.

Antibodies and Reagents.

The following antibodies were used: anti-I-A/I-E FITC (MHC Class II;M5/114.15.2); anti-Gr-1 PE (RB6-8C5); anti-CD11b PerCP-Cy5 (M1/70);anti-CD11c APC (N418); anti-CD4 FITC (GK1.5); anti-NK1.1 PE (PK136);anti-CD8a eFluor780 (53-6.7); anti-CD44 APC (IM7). All antibodies wereacquired from eBioscience (San Diego, Calif.). Liberase™ and DNAse I wasacquired from Roche. All media was from HyClone (Fisher).

Treatment with Antigenic Compositions.

Heat-killed K. pneumoniae with phenol (K. pneumoniae; lot KO12; 5.0OD600 units) was diluted 1/10 in PBS containing 0.4% phenol and 100 ulwas injected subcutaneously on day 0, 2, 4, and 6 into 5 mice.Heat-killed E. coli (lot; 5.0 OD600 units) was diluted 1/10 incontaining 0.4% phenol and 100 μl was injected subcutaneously on day 0,2, 4, and 6 into 5 mice. Control mice (n=5) were injected on day 0, 2,4, and 6 with PBS.

Brochoalveolar Lavage.

On day 7 mice were sacrificed and a bronchoalveolar lavage (BAL) wasperformed by exposing the trachea followed by insertion of a 22Gcatheter attached to a 1 ml syringe. 1 ml of PBS was injected into thelungs and removed and placed into a 1.5 ml microcentrifuge tube. Thelungs were subsequently washed 3 more times with 1 ml of PBS and thefluid was pooled. The first wash from each mouse was centrifuged at400×g and the supernatant was frozen for cytokine analysis. The final 3ml of lavage fluid was centrifuged and the cells were pooled with thecell pellet from the first lavage. The cells were counted and stainedwith antibodies specific for MHC class II, Ly6G/C, CD11b, and CD11c.After staining the cells were washed and analyzed on a FACS Calibur flowcytometer.

Lung Digestion.

After BAL was performed the lungs were placed in 5 ml of RPMI containing417.5 μg/ml Liberase TL (Roche) and 200 μg/ml DNAse I (Roche). The lungswere then digested at 37° C. for 30 mins. After digestion the lungs wereforced through a 70 μm cell strainer to create a single cell suspension.The cells were then centrifuged, washed, resuspended in FACS Buffer (PBSwith 2% FCS and 5 mM EDTA) and counted. After counting the cells werestained and analyzed by FACS using the same antibodies as for the BALcells.

Peritoneal Lavage.

1 ml of PBS was injected into the peritoneum of mice using a 1 mlsyringe attached to a 25G needle after BAL. The abdomen was massaged for1 minute and 0.5 ml of PBS was recovered from the peritoneum using a 1ml pipet. The lavage fluid was put in a 1.5 ml centrifuge tube,centrifuged at 400×g for 5 mins, and resuspended in FACS buffer prior tostaining and FACS analysis.

Spleen and Lymph Node Analysis.

The spleen and draining lymph node were removed after BAL and peritoneallavage and placed in PBS. The spleen was disrupted by mashing through a70 μm cell strainer (Fisher) and the lymph node was disrupted using therubber end of the plunger from a 1 ml syringe. After disruption, thesingle cell suspension from the spleen and lymph nodes was centrifuged,washed once with FACS Buffer, and resuspended in FACS Buffer prior tocounting, staining, and FACS analysis.

FACS Analysis.

Cells were stained on ice for 20 mins in 96 well plates using 50 μl ofantibodies diluted in FACS buffer. After 20 mins, 100 μl of FACs bufferwas added to the wells and the plates were centrifuged at 400×g for 5mins. Subsequently the media was removed and the cells were washed 1more time with FACS buffer. After the final wash the cells wereresuspended in 200 μl of FACS buffer and the data was acquired using aFACS Calibur flow cytometer (BD). A minimum of 20,000 live events werecollected for all samples except the BAL where a minimum of 5,000 eventswas collected.

The following results were obtained in this Example:

As illustrated in FIG. 18, mice were treated on day 0, 2, 4, and 6 witheither a K. pneumoniae antigenic composition, an E. coli antigeniccomposition or PBS. On day 7 the mice were sacrificed and the totalnumber of inflammatory monocytes (CD11 b+Gr-1+ cells) and dendriticcells (CD11c+ MHC class II+ cells) were determined by flow cytometry inthe peritoneal lavage fluid, lungs, lymph node and spleen. Error bars inFIG. 18 represent the standard deviation from 5 mice. *p-value <0.05using a Student's t-test.

FIG. 18 illustrates that treatment with a K. pneumoniae antigeniccomposition, but not an E. coli antigenic composition treatment,markedly increased the number of monocytes and DCs in the lungs of mice.In contrast to the lungs, K. pneumoniae did not lead to an increase inmonocytes in the peritoneum of the mice whereas E. coli did.Importantly, there was only a slight increase in the number ofinflammatory monocytes and no increase in DCs in the spleens of micetreated with either K. pneumoniae or E. coli suggesting that the effectsof the therapies are not general and are, in fact, specific for aparticular organ site. In addition to looking at the effects oftreatment on inflammatory monocytes and DCs in the lungs of mice, wealso looked at changes in other leukocytes such as cytotoxic CD8 Tcells, CD4 T helper cells, and natural killer (NK) cells all of whichcan potentially play a role in anti-tumour immunity.

FIG. 19 illustrates that a K. pneumoniae antigenic composition, but notPBS or an E. coli antigenic composition, resulted in a marked increasein the frequency and total numbers of NK cells, CD4 and CD8 T cells inthe lungs of treated mice. This Example is the first demonstration toour knowledge that subcutaneous injection of a killed bacterial specieswhich normally causes lung infection can promote the accumulation ofleukocytes in the lungs without the presence of any inflammation in thatsite. In addition, we have demonstrated that this effect is specific tothe targeted site and that it is also specific to the bacterialconstituents of the treatment used.

As illustrated in FIG. 19, mice were treated on day 0, 2, 4, and 6 witheither a K. pneumoniae antigenic composition, an E. coli antigeniccomposition, or PBS. On day 7, the mice were sacrificed and the totalnumber of CD4 T cells, CD8 T cells, and natural killer (NK) cells weredetermined by flow cytometry. Error bars represent the sd of valuesobtained from 5 mice per group. *p-value <0.05 using a Student's t-test.

Example 5C. Illustrating the Effects of Heat and Phenol InactivatedKlebsiella Pneumoniae (K. pneumoniae) Antigenic Compositions onAnti-Tumor Response in Mice, and the Status of Inflammatory Monocytesand Dendritic Cells Following Treatment in Tumor-Bearing Mice

The following methods and materials were utilized in this Example:

Tumour Cell Inoculations.

The Lewis lung carcinoma cell line derived from the C57BL/6 backgroundwere acquired from ATCC (Manassas, Va.). The cells were maintained inDulbecco's Modified Eagles Media (ATCC, Manassas, Va.) containing 10%FCS. The cells were grown in a humidified 37° C. incubator with 5% C02.Prior to tumour inoculation, cells were detached from culture platesusing 0.25% trypsin and 0.53 mM EDTA. The cells were washed in PBS andresuspended at 8×10⁶ cells/ml and 200 ul (4×10⁵ cells) was injectedintravenously into mice.

Treatment with Antigenic Composition.

The following antigenic compositions were used in this study: aheat-inactivated K. pneumoniae antigenic composition with phenol (lotKO12) and a phenol-inactivated K. pneumoniae antigenic composition (lotKO25). Both heat-inactivated K. pneumoniae and phenol-inactivated K.pneumoniae are concentrated to 5.0 OD600 units. 0.1 ml of K. pneumoniaediluted 1/10 in PBS with 0.4% phenol was injected subcutaneously every 2days starting on day 2 after tumour injection.

Analysis of Inflammatory Monocytes, DCs, T Cells, and NK Cells.

All analysis was done according to the methods used in Example 5B above.

TABLE 18 Experimental groupings and dose schedule for Example 5C LL/2Tumor Site of Concentration cells LL/2 of K. Pneumoniae ScheduleInjection Number of and Tumor (OD units) of Volume Date of Groupanimals/sex dose Injection Treatment Injections Treatment (ml) Sacrifice1A 5F 4 × 10⁵ Intravenous DPBSWP¹ None Once daily 0.1 Day 9 2A 5F LL/2HKWP² 0.05 on day 2, 3A 5F PHWP³ 0.05 4, 6, and 8 1B 5F DPBSWP¹ NoneOnce daily Day 16 2B 5F HKWP² 0.05 on day 2, 3B 5F PHWP³ 0.05 4, 6, 8,10, 12, 14, 1C 5F DPBSNP¹ None Once daily Day 23 2C 5F HKWP² 0.05 on day2, 3C 5F PHWP³ 0.05 4, 6, 8, 10, 12, 14, 16, 18, 20, 22 ¹Dulbecco'sPhosphate Buffered Saline with phenol ²Heat killed with phenol ³Phenolkilled with phenol

The following results were obtained in this Example:

This example was designed to determine if the presence of tumourimpacted the recruitment of cells to the lungs and whether the treatmenteffect increases over time resulting in further increases in cellrecruitment with ongoing treatment and thus, potentially, more optimaltherapeutic effect with prolonged treatment. In addition, we wanted todetermine whether a K. pneumoniae antigenic composition inactivated byphenol was more effective than a K. pneumoniae antigenic compositioninactivated by heat.

FIG. 20 clearly demonstrates that by day 9 (i.e., 4 treatments with a K.pneumoniae antigenic composition) there is already a marked increase inthe number of acute inflammatory monocytes, DCs, T cells, and NK cellsin the lungs of mice treated with a K. pneumoniae antigenic compositioninactivated by heat or phenol, many times greater than that of the lungsof mice treated with placebo (normal saline—PBS), again, clearlydemonstrating the marked targeted cellular immune response in the lungstriggered by K. pneumoniae antigenic composition therapy. On day 9,there was a suggestion that phenol inactivation was more effective thanheat inactivation, but this trend reversed by day 16. Importantly,however, with reference to the cell numbers in the lungs on day 9 andday 16, it is evident that there is a cumulative effect of bacterialtreatment on the recruitment of cells to the lungs. For example in thegroup treated with a phenol inactivated K. pneumoniae antigeniccomposition there are about 100,000 acute inflammatory monocytes in thelungs of the mice at day 9 and this number increases substantially to400,000 by day 16, demonstrating a substantially increasing responsewith ongoing treatment. The same increased treatment response withongoing treatment occurred in mice treated with heat inactivatedbacteria. Importantly, this cumulative treatment effect is observed forall other cell types analyzed as well. In this study, there was nodemonstrable statistically significant difference in immune cellrecruitment with heat or phenol inactivated K. pneumoniae antigeniccompositions.

As illustrated in FIG. 20, mice were injected with 4×10⁵ lewis lungcarcinoma cells intravenously on day 0. The mice were subsequentlytreated every other day starting on day 2 with a K. pneumoniae antigeniccomposition generated by heat inactivation, or phenol inactivation, orwith PBS. On day 9 and day 16 the mice were sacrificed and the totalnumbers of (A) inflammatory monocytes (CD11 b+Gr-1+) and DCs (CD11c+lab+) or (B) CD4 T cells, CD8 T cells, and natural killer (NK) cellswere determined by flow cytometry. Bars represent respectively: the PBStreated group, the mice treated with a heat-inactivated K. pneumoniaeantigenic composition and mice treated with a phenol-inactivated K.pneumoniae antigenic composition. Error bars represent the sd of valuesobtained from 5 mice per group. *p-value <0.05 using a Student's t-test.

The results of this study demonstrate an increasing immune responsewithin the targeted tissue with ongoing treatment.

Example 5D. Illustrating the Effects of Heat, Irradiation, and PhenolInactivation on K. pneumoniae Antigenic Compositions, IncludingLeukocyte Recruitment into the Lungs of Mice, and the Effects of Phenolas a Preservative has any Effects

The following methods and materials were utilized in this Example:

Mice.

C57BL/6 female mice 7-8 weeks of age were ordered from Harlan Labs(Livermore, Calif.) for these studies.

Antigenic Compositions.

Heat killed K. pneumoniae antigenic composition with phenol (KO12), heatkilled K. pneumoniae antigenic composition without phenol (KO25),irradiated K. pneumoniae antigenic composition without phenol (KO24),and phenol killed K. pneumoniae antigenic composition without phenol(KO25) were used in this study. All bacterial formulations were at aconcentration of 5.0 OD units in saline. For 1/10 dilution, 1 ml ofbacterial formulation was added to 9 ml of DPBS and mixed immediatelyand then again prior to injection. For 1/100 dilution, 0.1 ml ofbacterial formulation will be added to 9.9 ml of DPBS and mixedimmediately and then again prior to injection. For dilutions ofheat-killed Klebsiella pneumoniae antigenic composition with phenol, thedilutions were carried out as above using a DPBS solution containing0.4% phenol (w/v). To prepare the 0.4% phenol in DPBS, first a 5% phenolsolution was prepared by adding 0.5 g of solid phenol (Sigma Aldrich,St. Louis, Mo.) to 10 ml of DPBS (Hyclone, Logan, Utah) This solutionwas filtered through a 0.22 um filter (Millipore, Billerica, Mass.) andstored at 4° C. Immediately prior to use the 5% phenol solution wasdiluted 1 ml in 12.5 ml DPBS and used to prepare the bacterialformulations.

Treatment with Antigenic Compositions.

5 mice per group were treated subcutaneously on day 0, 2, 4, and 6 with0.1 ml of a heat-killed K. pneumoniae antigenic composition diluted 1/10in PBS or PBS with 0.4% phenol, 0.1 ml of an irradiated K. pneumoniaeantigenic composition diluted 1/10 in PBS, or a phenol inactivated K.pneumoniae antigenic composition diluted 1/10 with PBS or PBS with 0.4%phenol. On day 7 the mice were sacrificed and leukocyte recruitment tothe lungs was analyzed as in Example 5B.

The following results were obtained in this Example:

In this example, we used leukocyte recruitment to the lungs as asurrogate of efficacy to compare the efficacy of K. pneumoniae antigeniccompositions inactivated by various methods. FIG. 21 illustrates that,for both heat killed and phenol killed K. pneumoniae antigeniccompositions, the addition of phenol (0.4%) as a preservative, increasedefficacy, as measured by cellular recruitment. In some embodiments, asmall amount of phenol (i.e., 0.4% as a preservative) may stabilize acomponent of the bacterial cell wall, for example a component that isimportant in antigen pattern recognition and activating an optimaltargeted response. In comparing the 3 formulations containing phenol asa preservative (i.e., heat killed, phenol killed and radiation killed),irradiated K. pneumoniae antigenic composition led to the greatestrecruitment of acute inflammatory monocytes, DCs, NK cells, and T cellsto the lungs, followed by phenol killed K. pneumoniae antigeniccomposition, with heat killed K. pneumoniae antigenic compositionresulting in the least cellular recruitment.

As illustrated in FIG. 21, mice were treated on day 0, 2, 4, and 6 withK. pneumoniae antigenic composition inactivated by heat (HKWP) orwithout (HKnp) phenol preservative, inactivated with phenol with (PKWP)or without (PKnp) phenol preservative, or K. pneumoniae antigeniccomposition inactivated by irradiation with phenol preservative (IRWP).On day 7 the mice were sacrificed and the total numbers of (A)inflammatory monocytes (CD11 b+Gr-1+) and DCs (CD11c+ lab+) or (B) CD4 Tcells, CD8 T cells, and natural killer (NK) cells were determined byflow cytometry. Error bars represent the sd of values from 5 mice pergroup. *p-value <0.05 compared to mice treated with IRWP using aStudent's t-test.

Example 6: Clinical Studies Involving Advanced Epithelial CancersOverview of Treatment

The following patients with different advanced cancers have undergonetreatment with heat inactivated targeted bacterial antigeniccompositions. Fully informed written consent was received for eachpatient and in every case. The treatment consisted of repeated (3×/week)subcutaneous injections of exact amounts of the vaccine in the abdominalregion. The dosage was gradually increased in each patient to achieve asufficient skin response (3-5 cm redness lasting for ca. 24 h). For eachpatient a case report form (CRF) documented skin reaction and possibleclinical effects and/or side effects related to the treatment.Characteristic and concomitant treatments as well as the response totherapy of the patients are briefly described.

Patient #1:

53 y old male patient with advanced melanoma, ICD10: C43, 1st diagnosed11/2005 lesion under right big toe nail, histology one year later12/2006: advanced malignant melanoma; patient refused amputation of thebig toe; 5/2008 lymphatic metastasis to the right leg, at the time offirst presentation for targeted bacterial antigenic compositiontreatment (9/2008) leg swollen with 100% increase in circumference:Karnofsky 80%, no pretreatment.

Treatments over 6 month 09/2008-04/2009:

-   -   12× intraperitoneal Ozone (O3) insufflation;    -   42× locoregional radiofrequency hyperthermia (13.56 Mhz);    -   18× moderate whole body hyperthermia 38.5° C.;    -   6 month treatment with Staph. aureus antigenic composition s.c.;    -   Orthomolecular medicine: high dose vitamin C infusions (0.5        g/kg/BW), Vitamin D3; 2.000 iu/day, Artesunate 200 mg/day,        Celebrex 100 mg/day, low dose naltrexone, medical; mushroom        (cordyceps, reishi, shitake), selenium 200 uc/day, curcumin        3.000 mg/day, proteolytic enzymes (Wobemugos)

Epicrisis Details:

-   -   PET 7/2008: SUV in right big toe 4.81, knee: 5.01    -   PET 12/2008: SUV in right big toe 3.80, knee: 4.02    -   We started treatment end of 9/2008.    -   At that time (9/2008) there were clinically already lymph nodes        in the groin palpable which were not seen on the PET from        7/2008.    -   05/2010: good clinical condition, PET confirms complete        remission, Kamofsky 100%.

Patient #2:

48 y old female patient with advanced bilateral breast cancer, ICD10:C50.9 1st diagnosed 4/2008; histology ductal infiltrating adenocarcinomaof the breast, ER/PR pos., Her2 not known, T1/T2, N1 (sentinel nodeaxilla), M0 G3; multiple treatments with sodium bicarbonate injectionsand repeated surgery to both breasts; patient refused the proposedbilateral mastectomy and was never resected “in sano” (e.g., margins ofthe lumpectomies were never free of tumor cells). Patient also refusedChemotherapy and/or hormone therapy. Kamofsky 90%, no pretreatment.

Treatments over 8 month 03/2009-11/2009:

-   -   3× autologous Dendritic cell therapy in combination with:    -   3× long-duration moderate whole body hyperthermia 40⁰ over 8 h    -   57× locoregional radiofrequency hyperthermia to both breasts        (13.56 Mhz)    -   6 month treatment with Staph. aureus antigenic composition s.c.    -   Orthomolecular medicine: high dose vitamin C infusions (0.5        g/kg/BW), low dose naltrexone, medical mushroom (cordyceps,        reishi, shitake), curcuma 3.000 mg/day, zinc

Epicrisis Details:

-   -   Treatment started end of 3/2009.    -   05/2010: bilateral breast MRI shows no abnormality detected,        good clinical condition, Karnofsky 100%

Patient #3:

73 y old female patient with advanced NSCLC cancer FIGO IIc, ICD10: C34,1st diagnosed 6/2009; histology clear cell adenocarcinoma of the lungs,T4, N1, M0 G3; she underwent neoadjuvant CHT; the restaging after 3cycles neoadjuvant CHT demonstrated T2 tumor; she then underwent leftpneumectomy R0 resection and mediastinal lymphadenectomy; Karnofsky 90%.

Treatments over 7 month 08/2009-03/2010:

-   -   08/2009 Began chemotherapy with Taxan/Cisplatin until 10/2009 in        combination with:    -   4× long-duration moderate whole body hyperthermia 40⁰ over 8 h        (1-2/2009)    -   20× locoregional radiofrequency hyperthermia to the thorax        (13.56 Mhz) (8-10/2009)    -   10/2009 le Pneumectomy R0 resection (Oncology decided against        further adjuvant CHT)    -   6 month treatment with Klebsiella pneumoniae antigenic        composition s.c. (08/2009-02/2010)    -   Orthomolecular medicine: thymus peptides i.m., indometacin,        cimetidine, high dose vitamin C infusions (0.5 g/kg/BW), ALA/N        protocol (low dose naltrexone and alpha lipoic acid), medical        mushroom (reishi), curcuma 3.000 mg/day, zinc, melatonin,        inhalation of ionized oxygen

Epicrisis details:

-   -   Started treatment end of 08/2009.    -   05/2010: CT Thorax and Tumor marker CEA, NSE and CYFRA show        complete remission, good clinical condition, Kamofsky 100%.

Patient #4:

50 y old female patient with advanced Breast cancer, ICD10: C50, withdisseminated hepatic and pulmonary metastasis, 1st diagnosed 8/1990;histology undifferentiated cirrhoses type adenocarcinoma of the breast,pT1c, N1, M0 G3; she underwent multiple chemotherapy courses over 20years; 11/2004 first scar reoccurrence, 12/2004 ablation left breast, 6×CHT Epitax and radiation of thoracic wall; 9/2005 1st diagnosis ofdisseminated liver and pulmonary metastases: again 8× CHT with Epitaxuntil 3/2006. Restaging showed progressive disease at which time shebegan targeted bacterial antigenic composition treatment. Karnofsky 90%.

Treatments over 4 years 03/2006-03/2010:

-   -   03/2006 Began treatment with Polyvaccinum forte vaccine in        combination with:    -   3× autologous Dendritic cell therapy in combination with        (6-8/2006):    -   3× long-duration moderate whole body hyperthermia (LD-WBH) 40⁰        over 8 h (1-2/2009)    -   25× locoregional radiofrequency hyperthermia to the thorax &        liver (13.56 Mhz) (3-6/2006)    -   8 month treatment with Klebsiella pneumoniae antigenic        composition (11/2008-7/2009)    -   10/2009 TM CEA and CA15/3 started rising again    -   02-03/2009 2× autologous Dendritic cell therapy without LD-WBH    -   04/2010 thermal ablation of liver mets (No change of lung        metastasis)    -   Orthomolecular medicine: thymus peptides i.m., indometacin,        cimetidine, high dose vitamin C infusions (0.5 g/kg/BW), curcuma        3.000 mg/day, zinc, proteolytic enzymes

Epicrisis Details:

-   -   We started treatment end of 03/2006.    -   05/2010: CT Thorax show stable disease over 4 years, progressive        disease of liver mets, good clinical condition, Karnofsky 100%.

Patient #5:

66 y old male patient with advanced prostate cancer, ICD10: C61, withdisseminated bone and lymphatic metastasis, 1st diagnosed 01/1997;histology undifferentiated adenocarcinoma of the prostate, pT3, N1, M1G3; he underwent multiple Hormone- and CHT over 13 years; patient is ingood clinical condition surviving metastatic prostate cancer for 13years since diagnosis; Kamofsky 90%.

Treatments over 11 years 11/1999-05/2010:

-   -   13 years anti-androgen with Suprefact, Zoladex, Casodex,        Trenantone, Estracyt, B-Sitosterol    -   06/2006-12/2007 Began Mixed bacterial vaccine treatment with        Polyvaccinum forte vaccine    -   Since 03/2008 regular chemotherapy with Taxotere 140 mg every        3-4 weeks    -   50× moderate whole body hyperthermia 39° over 3 h (1999-2009)    -   18 month treatment with Staph. aureus antigenic composition        (11/2008-05/2010, ongoing)    -   05-06/2009 2× autologous Dendritic cell therapy without moderate        WBH 390, 3 h    -   Orthomolecular medicine: wheat grass, cimetidine, Zometa, high        dose vitamin C infusions (0.5 g/kg/BW), curcuma 3.000 mg/day,        boswellia serrata (Indian) 400 mg 4×4/day, zinc, proteolytic        enzymes

Epicrisis Details:

-   -   We started treatment end of 1999.    -   05/2010: Bone scan shows stable disease; PSA currently 89 ng/ml,        good clinical condition, Kamofsky 90%.

Patient #6:

52 y old female patient with advanced primary cancer of the peritoneum,ICD10: C48.2, with disseminated peritoneal carcinosis, 1st diagnosed06/2003; histology undifferentiated adenocarcinoma of the peritoneum,pT3, N1, M1 G3; she underwent Debulking OP with ovarectomy bilaterly andhysterectomy and adjuvant chemotherapy with Taxol/Paraplatin:progressive disease and change to Taxol/Paraplatin with SD until 8/2008;progressive disease with disseminated peritoneal LK metastasis and 3rdline CHT with Carboplatin and beginning of treatment with targetedbacterial antigenic composition; patient was in good clinical condition;Karnofsky 100%.

Treatments over 4 month 05-09/2009:

-   -   5× Carboplatin chemotherapy (3rd line) followed by:    -   5× long-duration moderate whole body hyperthermia (LD-WBH) 40°        over 8 h (05-09/2009)    -   20× locoregional radiofrequency hyperthermia to the abdomen        (13.56 Mhz) (05-09/2009)    -   2 month treatment with E. coli (colon) antigenic composition        (05-07/2009)    -   Orthomolecular medicine: high dose vitamin C infusions (0.5        g/kg/BW), high dose artichoke and sylimarin extracts (liver)

Epicrisis Details:

-   -   We started treatment end of 5/2009.    -   04/2010: CT abdomen and tumour marker demonstrate complete        remission; good clinical condition, Kamofsky 100%

Patient #7:

50 y old female patient with inoperable pancreatic cancer, ICD10: C25.9,with the cancer infiltrating the large vessels; Sonographic and CTevidence suggested invasion into superior mesenteric vein. firstdiagnosed 02/2009; histology undifferentiated adenocarcinoma of thepancreas, pT3, N1, M1 G3 with peritoneal carcinosis; she underwent localradiation and low dose Xeloda as radiation sensitizer; when she begantreatment at our clinic the cancer was still unresectable; Karnofsky100%.

Treatments over 2 month 06-07/2009: (E. coli SSI for 11 months)

-   -   1× autologous NDV-primed Dendritic cell therapy in combination        with:    -   1× long-duration moderate whole body hyperthermia 40° over 8 h        (7-10/2009)    -   4× moderate whole body hyperthermia 38.5°    -   15× locoregional radiofrequency hyperthermia to the abdomen        (13.56 Mhz) (06-07/2009)    -   11 months treatment with E. coli (colon) antigenic composition        (06/2009 until today, ongoing)    -   Orthomolecular medicine: thymus peptides i.m; medical mushroom        (reishi, cordyceps, shitake) high dose vitamin C infusions (0.5        g/kg/BW), high dose proteolytic enzyme therapy (wobenzym        phlogenzym), cimetidine.

Epicrisis Details:

-   -   We started treatment end of 6/2009.    -   05/2010: complete remission, NED; PET 02/2010 demonstrated no        glucose uptake; tumour marker normal CA19/9: 4; good clinical        condition, Karnofsky 100%

Example 7: Dosage Studies (QB28 Study)

In an effort to examine the role of dosing, mice were treated witheither different doses of K. pneumoniae antigenic composition or a PBScontrol. All mice (C57BL/6) began treatment with K. pneumoniae_antigeniccomposition or PBS on day −10, −8, −6, −4 and −2 using the followinginjection sites (1^(st) injection: ventral inguinal right; 2^(nd)injection: ventral axillary right, 3^(rd) injection: ventral axillaryleft; 4^(th) injection: ventral inguinal left etc.). All mice thenreceived a tumor inoculation dose of 3×10⁵ Lewis Lung carcinoma cellsvia intravenous injection into the lateral tail vein of the mice. Thedoses of antigenic compositions or PBS were as follows: i) PBS 0.1 ml;ii) K. pneumoniae 0.1 mL of OD600=1.67; iii) K. pneumoniae 0.1 mL ofOD600-0.5. Mice received K. pneumoniae antigenic compositions or PBS,treatment on days 2, 4, 6, and 8. The experiment was termination on day10; all mice were sacrificed, their lungs were surgically removed,rinsed in water, weighed, and then placed into Bouins fluid for fixationand counting 24 hours later. As shown in FIG. 22, each data pointrepresents the number of tumour nodules from one mouse. Photographs ofrepresentative lungs from these experiments are shown in FIG. 23. FIG.23 shows that the lungs from mice treated with the PBS control showsignificant numbers of nodules. By way of comparison, FIG. 23demonstrates that the lungs from mice treated with K. pneumoniaeantigenic composition shows fewer numbers of nodules at a rateequivalent to those shown in FIG. 22.

QB30 Study.

In further studies on the effect of dosage of K. pneumoniae antigeniccompositions, it was demonstrated that if a dosage of a K. pneumoniaeantigenic composition is too low, it is not effective for the treatmentof lung cancer. In these studies, the results of which are shown in FIG.24, all mice (C57BL/6) began treatment with K. pneumoniae antigeniccomposition or PBS on day −10, −8, −6, −4 and −2 using the followinginjection sites (1^(st) injection: ventral inguinal right; 2^(nd)injection: ventral axillary right, 3′ injection: ventral axillary left;4^(th) injection: ventral inguinal left etc.). All mice then received atumor inoculation dose of 3×10⁵ Lewis Lung carcinoma cells viaintravenous injection into the lateral tail vein of the mice. The dosesof antigenic compositions or PBS was as follows: i) PBS 0.1 ml; ii) K.pneumoniae 0.1 mL of OD600=0.5; iii) K. pneumoniae 0.1 mL of OD600-0.05.Mice continued to receive K. pneumoniae antigenic compositions, or PBS,treatment on day 2, 4, 6, 8, 10, 12, 14, and 16. The experiment wastermination on day 18; all mice were sacrificed, their lungs weresurgically removed, rinsed in water, weighed, and then placed intoBouins fluid for fixation and counting 24 hours later. As shown in FIG.24, each data point represents the number of tumour nodules from onemouse.

The results from the QB28 and QB30 studies suggest that extremely highdoses of K. pneumoniae antigenic compositions are ineffective, perhapsdue to over-stimulation of the host immune system. The results fromthese studies also suggest that low doses are ineffective, perhaps dueto insufficient stimulation of the host immune system.

Example 8: Cisplatin Efficacy Studies

In an effort to examine the role between Cisplatin and chemotherapy anddoses of K. pneumoniae antigenic compositions, the QB38 study wascompleted. Briefly, all mice received a tumor inoculation dose of 3×10⁵Lewis Lung carcinoma cells via intravenous injection into the lateraltail vein on day 0 of the study. Following this inoculation, all micewere pooled into a single cage and subsequently distributed into theirrespective cages at random to control against biased data. On themorning of day +2 of this study, mice within the Cisplatin group wereinjected with 10 mg/kg of this drug intraperitoneally. Control mice wereinjected with control (PBS). Thereafter, on the afternoon of day +2 ofthis study, mice received K. pneumoniae antigenic compositions, or PBS;these injections continued on days 4, 6, 8, 10, and 12. The study wasterminated on day 14; thereafter, all mice were sacrificed, their lungswere surgically removed, rinsed in water, weighed, and then placed intoBouins fluid for fixation and counting 24 hours later. As shown in FIG.25, each data point represents the number of tumour nodules from onemouse based on whether the mice were treated with PBS, K. pneumoniaeantigenic compositions, K. pneumoniae antigenic compositions combinedwith Cisplatin, or Cisplatin alone. The results summarized in FIG. 25indicate that there were fewer nodules in mice treated with K.pneumoniae antigenic compositions and Cisplatin compared with thosetreated with Cisplatin alone, K. pneumoniae antigenic compositionsalone, or the PBS control.

A further study was designed to determine whether K. pneumoniaeantigenic composition therapy could work in synergy with platinum-basedchemotherapy to extend the survival of mice bearing pulmonary Lewis Lungtumors. Four groups of five C57BL/6 female mice all received 10⁵ LewisLung carcinoma cells i.v. on day 0. On day 2, groups 3 and 4 received asingle i.p. dose of 10 mg/kg Cisplatin. Beginning on day 4 the micereceived either K. pneumoniae or placebo (PBS) every 2 days until death.FIG. 26 illustrates the survival of all of the mice and the table showsthe p-values of the various survival curves calculated using theLog-rank Test. Treatment of mice with Cisplatin alone increased thesurvival of mice with lung tumors with median survival increasing from16 days in the PBS group to 23 days in the PBS+Cisplatin group.Treatment with K. pneumoniae alone also increased survival of the micecompared to PBS (median survival 19 days for K. pneumoniae vs. 16 daysfor PBS). Most importantly Cisplatin chemotherapy together with K.pneumoniae therapy had the greatest therapeutic benefit (median survivalof 32 days) demonstrating the synergy between platinum-basedchemotherapy and antigenic composition therapy in a mouse model of lungcancer. The p-values for the data generated in this QB45 study are shownin Table 19 below.

TABLE 19 Survival Date (QB45) K. pneumoniae + PBS K. pneumoniae PBS +cisplatin cisplatin Median 16 19 23 32 survival (days) P value (to 0.0370.002 0.002 PBS) P value (to 0.008 PBS + cisplatin)

As shown in this Example, antigenic compositions can be used on the sameday as Cisplatin or at a period after Cisplatin administration. As usedherein, the term “antigenic composition” refers to a composition thatincludes antigens of one or more microbial species. As used herein, theterm “microbial species” may refer to a viral pathogen or a bacterialpathogen or a fungal pathogen, as detailed herein.

A further study was designed to explore whether there is any synergybetween platinum based chemotherapy and K. pneumoniae antigeniccomposition therapy for the treatment of lung cancer in mice. All of themice received 10⁵ Lewis Lung carcinoma cells iv on day 0. The micereceived antigenic compositions or PBS subcutaneously every 2 daysstarting on day 0. On day 12, some of the mice were treated withcisplatin (10 mg/kg) intraperitoneally. The following day (day 13), 3mice from each group were bled and the blood cells were stained withanti-CD1 b antibody and analyzed by FACS. The plots in FIG. 27 depictthe frequency of CD11 b+ myeloid cells in the blood on day 13. Eachpoint represents a single mouse. The results of this study demonstratethat antigenic composition therapy can enhance the frequency of myeloidcells (monocytes, macrophages, granulocytes, dendritic cells) in theblood when given with cisplatin. This may enhance immunity in theanimals by providing a greater number of these innate myeloid cellswhich are capable of responding to the tumors or pathogens. In addition,since bone marrow suppression is a clinically important side-effect ofchemotherapy treatment, with resultant reduction in myeloid cells in theblood, which can result in postponement/discontinuation of chemotherapyor susceptibility to infection, the enhancement of myeloid cells withantigenic composition therapy during chemotherapy, may be helpful toreduce the risk of this important and clinically relevant side effect ofchemotherapy.

Example 9: Macrophage Studies (MOA13 Study)

To examine the role of macrophages with respect to embodiments of theinvention, the MOA13 study was completed. Briefly, mice were eitherinoculated with 3×10⁵ Lewis Lung carcinoma cells or were injected withHBSS as a vehicle control. For mice inoculated with Lewis Lung carcinomacells, they were pooled into a single cage where they were subsequentlytransferred at random to their respective cages. Thereafter, mice weretreated with either K. pneumoniae antigenic compositions, or PBS, ondays 2, 4, 6 and 8. Thereafter, all mice were sacrificed on day 9. Toobtain information with respect to myeloid and NK cell frequencies, 20mice (5 from each group) had their lungs surgically removed, and thelungs were digested using Liberase TL and DNAse. Following the digestingand cell preparation, a single cell suspension was generated.Thereafter, a portion of the cells were transferred into 96 round bottomplates for staining using myeloid specific antibodies (CD11b+, NK1.1+)and NK specific antibodies (NK1.1+, CD11b+). For the former cell type,gates were used to select only CD11 b+ and NK1.1− cell populations.Thereafter, cell data acquisition was performed using BD FACSCalibur andanalysis was performed using FlowJo. Statistical analysis and graphicalrepresentation was performed using Excel and GraphPad Prism. The resultsare shown in FIG. 28. Briefly, treatment with K. pneumoniae antigeniccompositions leads to an increase in both myeloid cells (likelymonocytes and macrophages) as well as CD11 b+NK cells in the lungs ofmice so treated.

With a focus of obtaining information with regard to cytokines beingproduced within lung tissue, the following experiments were conducted.Mice were either inoculated with 3×10⁵ Lewis Lung carcinoma cells orwere injected with HBSS as a vehicle control. For mice inoculated withLewis Lung carcinoma cells, they were pooled into a single cage wherethey were subsequently transferred at random to their respective cages.Thereafter, mice were treated with either K. pneumoniae antigeniccompositions, or PBS, on days 2, 4, 6 and 8. Thereafter, all mice weresacrificed on day 9. To obtain information re: cytokine within lungtissue, a bronchoalveolar lavage was performed on the lungs. Thereafter,the lungs were surgically removed immediately after the lavage andplaced into pre-weighed vials containing PBS and protease inhibitors.Thereafter, the lung tissue was homogenized, centrifuged, and thesupernatant was applied to ELISA kits (eBioscience); the ELISA assay wascarried out according to manufacturer's guidelines. Statistical analysisand graphical representation was performed using Excel and GraphPadPrism. Data is represented as pg of cytokine per mg of original lungtissue. Each data point in FIG. 29 is the value from a single mouse. Asshown in FIG. 29, treatment with K. pneumoniae antigenic compositionsleads to an increase in anti-tumour (IL-12, MCP-1, GMCSF, IL-6) cytokineproduction in the lung tissue.

With a focus of obtaining information with regard to cytokine productionin the bronchoalveolar lavage (BAL) fluid, the following experimentswere conducted. Mice were either inoculated with 3×10⁵ Lewis Lungcarcinoma cells or were injected with HBSS as a vehicle control. Formice inoculated with Lewis Lung carcinoma cells, they were pooled into asingle cage where they were subsequently transferred at random to theirrespective cages. Thereafter, mice were treated with either K.pneumoniae antigenic compositions, or PBS, on days 2, 4, 6 and 8 of theexperiment. Thereafter, all mice were sacrificed on day 9. To obtaininformation with regard to cytokine production in the lungs,bronchoalveolar lavage was performed on the lungs of the mice. The fluidfrom the lavage was placed into vials, and stored at −80° C. until atime when ELISA assay was performed. Thereafter, the ELISA assay wascarried out according to manufacturer's guidelines. Statistical analysisand graphical representation was performed using Excel and GraphPadPrism. Data is represented as pg/ml of lavage fluid as shown in FIG. 30.Each data point represents the value obtained from one mouse. As shownin FIG. 30, treatment with K. pneumoniae antigenic compositions had noeffect on cytokine production in the BAL fluid.

With a focus on examining the M1/M2 macrophage phenotypes in the modeldescribed herein, NOS2 and Arg1 levels were monitored in the lung. Theexperiments conducted were as follows: briefly, mice were eitherinoculated with 3×10⁵ Lewis Lung carcinoma cells or were injected withHBSS as a vehicle control. For mice inoculated with Lewis Lung carcinomacells, they were pooled into a single cage where they were subsequentlytransferred at random to their respective cages. Thereafter, mice weretreated with either K. pneumoniae antigenic compositions, or PBS, ondays 2, 4, 6 and 8 of the experiment. Thereafter, all mice weresacrificed on day 9. To obtain information with respect to NOS2 and Arg1gene expression, 20 mice (5 from each group) had their lungs surgicallyremoved. Thereafter, a small portion of these lungs were cut usingsterile techniques and placed into RNAlater to stabilize the RNAmaterial for future gene analysis. Total RNA was extracted from the lungtissue using a kit from Qiagen and used according to manufacturer'sprotocol. A cDNA kit was used to convert an amount of RNA into cDNA(Qiagen), again by following instructions supplied by manufacturer. qPCRwas conducted using primers designed to specifically amplify Nos2 andArg1 (Nos2: forward—CGCTTTGCCACGGACGAGA; reverse—AGGAAGGCAGCGGGCACAT;Arg1: forward—GGTCCACCCTGACCTATGTG; reverse—GCAAGCCAATGTACACGATG).Statistical analysis was conducted using Excel and GraphPad Prism. Asshown in FIG. 31, treatment with K. pneumoniae antigenic compositionsleads to an increase in the Nos2/Arg1 ratio in the lungs, whichcorrelates with an enhanced anti-tumour response.

With a focus on investigating the M1/M2 response in the in vivo modeldescribed herein, the expression of CD206 (mannose receptor) wasmonitored. Briefly, mice were either inoculated with 3×10⁵ Lewis Lungcarcinoma cells or were injected with HBSS as a vehicle control. Formice inoculated with Lewis Lung carcinoma cells, they were pooled into asingle cage where they were subsequently transferred at random to theirrespective cages. Thereafter, mice were treated with either K.pneumoniae antigenic compositions, or PBS, on days 2, 4, 6 and 8 of theexperiment. Thereafter, all mice were sacrificed on day 9. To obtaininformation with regard to CD206 expression, 20 mice (5 from each group)had their lungs surgically removed, and digested using Liberase TL andDNAse. Following the digesting and cell preparation, a single cellsuspension was generated. A portion of the cells were transferred into96 round bottom plates for staining using CD206 specific antibodies(clone MR5D3), acquired from Cedarlane Labs (Burlington, ON). As CD206is located both intra- and extracellularly, the cells were first fixedusing paraformaldehyde, and staining with the antibody inpermeabilization solution. Analysis was performed using FlowJo.Statistical analysis and graphical representation was performed usingExcel and GraphPad Prism. The results are shown in FIG. 32. As shown inFIG. 32, treatment with K. pneumoniae antigenic compositions leads to areduction in CD206 expression on lung macrophages both in the presence(PBS+LL2 and K. pneumoniae 1/10×+LL2) or absence of lung tumours (PBSand K. pneumoniae 1/10×). In the presence of lung cancer, K. pneumoniaeantigenic compositions reduce the frequency of CD206 expression fromabout 20% (PBS+LL2 group) to about 10% (K. pneumoniae 1/10×+LL2 group).A similar reduction in CD206 expression was seen in K. pneumoniaetreated animals without any lung cancer (PBS and K. pneumoniae 1/10×).

With a focus on investigating the M1/M2 phenotypes in the in vivo modeldescribed herein, the expression of F4/80+ macrophages was monitored.Briefly, mice were either inoculated with 3×10⁵ Lewis Lung carcinomacells or were injected with HBSS as a vehicle control. For miceinoculated with Lewis Lung carcinoma cells, they were pooled into asingle cage where they were subsequently transferred at random to theirrespective cages. Thereafter, mice were treated with either K.pneumoniae antigenic compositions, or PBS, on days 2, 4, 6 and 8 of theexperiment. Thereafter, all mice were sacrificed on day 9. To obtaininformation with respect to F4/80+ expression in macrophages, 20 mice (5from each group) had their lungs surgically removed, and digested usingLiberase TL and DNAse. Following digesting and cell preparation, asingle cell suspension was generated. A portion of the cells weretransferred into 96 round bottom plates for staining using F4/80monoclonal antibodies. Cell data acquisition was performed using BDFACSCalibur. Analysis was performed using FlowJo. Statistical analysisand graphical representation was performed using Excel and GraphPadPrism. As shown in FIG. 33, treatment with K. pneumoniae antigeniccompositions leads to a reduction in F4/80+ macrophages in the lungs.This reduction is thought to correlate with a reduction in M2-likemacrophages.

Example 10: Site Specificity Studies (MOA14 Study)

With a focus on investigating the M1/M2 phenotypes in the in vivo modeldescribed herein which is used in conjunction with the antigeniccompositions described herein, the following experiments were performed.Briefly, 5 mice per group were treated on day 0, 2, 4, and 6 with eitherPBS, E. coli colon antigenic compositions, or K. pneumoniae antigeniccompositions. On day 7 of the experiment, the mice were sacrificed and abronchoalveolar lavage was performed. Subsequently the lungs andproximal colon were removed and enzymatically digested. After digestion,the recovered cells were washed and stained with antibodies specific forI-A/I-E FITC (MHC class II; M5/114.15.2); anti-Gr-1 PE (RB6-8C5_;anti-CD11b PerCP-Cy5 (M1/70); anti-CD11c APC (N418). All antibodies wereacquired from eBioscience (San Diego, Calif.). The lung cells werecounted to determine the total number of cells (the colon was notcounted because we did not remove equal amounts of colon betweensamples). After staining for 20 mins the cells were washed and analyzedby FACS. Each data point shown in corresponding FIG. 34 represents thefrequency of CD11b+Gr-1+ cells in the live gate for one mouse. As shownin FIG. 34, treatment with E. coli antigenic compositions leads to anincreased frequency of inflammatory monocytes in the colon of treatedmice.

Further, and as shown in FIG. 35, when monocytes in the lungs wereexamined based on the experimental methods detailed herein, it was foundthat while both E. coli and K. pneumoniae antigenic compositionsincrease the frequency of monocytes in the lungs of mice, K. pneumoniaeantigenic compositions were more effective when counting for totalnumbers. Referring to FIG. 35, the left-most panel shows the frequencyof CD11b+Gr-1+(inflammatory monocyte) cells in the lungs; the right-mostpanel shows the total number of CD11 b+Gr-1+ cells in the lung.

In an effort to examine the phenotype of macrophages present in tumoursusing the in vivo model described herein which is used in conjunctionwith the antigenic compositions described herein, M1-like and M2-likemacrophages were examines. As shown in FIG. 36, this Figure representsthe frequency of M1-like (see left panel of FIG. 36) TAMs (tissueassociated macrophages) or M2-like (see right panel of FIG. 36) in subQ4T1 tumours on day 8 post tumour implantation. As detailed herein,M1-like macrophages were defined as being CD1l b+/Gr-1-/MHC Class IIhigh; M2-like macrophages were defined as being CD11 b+/Gr-1-/MHC ClassII low.

Example 11: Indomethacin Efficacy and Anti-Inflammatory Studies

In an effort to examine the efficacy of combining antigenic compositiontreatment with indomethacin. Briefly, experiments were designed whereinthere were 10 or 11 mice in each of 4 groups with all treatmentsbeginning on day 4 after tumour inoculation. All mice received 50,0004T1 mammary carcinoma cells subQ on day 0. Thereafter, the 4 groups weretreated as follows: 1) Indomethacin daily (in drinking water)+PBS subQevery 2 days; 2) Indomethacin daily (in drinking water)+S. aureusantigenic composition subQ every 2 days; 3) Control vehicle daily (indrinking water)+PBS subQ every 2 days; and 4) Control vehicle daily (indrinking water)+S. aureus antigen composition subQ every 2 days. Withrespect to FIG. 37, the left-most panel of the Figure demonstrates thetumour volume for the various groups on day 15 of the experiment. Theright-most panel demonstrates the frequency and makeup of the CD11 b+cells in the tumors on day 11 of the experiment. The frequency of CD11b+cells is significantly increased in both of the Indomethacin treatedgroups relative to the control. These results demonstrate the efficacyof combining Staph. aureus antigenic compositions withanti-inflammatories, such as indomethacin. Further, and as shown in FIG.38 herein, at the day 22 time point, indomethacin treatment resulted inan increase in CD11 b+ cells.

To further examine the efficacy of combining antigenic compositiontreatment with indomethacin, a study was designed. Briefly, four (4)groups of 10-11 Balb/c mice per group received 10,000 4T1 carcinomacalls SQ on day 0. Thereafter, treatments were as follows: the firstgroup received indomethacin (14 pg/ml in water) starting on day 4+PBS ondays 4, 6, 8 etc.; the second group received indomethacin (14 μg/ml inwater) and S. aureus antigenic compositions [0.1 ml of 0.5 OD 600 nmstock] starting on day 4+PBS on days 4, 6, 8 etc.; the third groupreceived PBS starting on days 4, 6, 8 etc.; and the fourth groupreceived S. aureus antigenic compositions [0.1 ml of 0.5 OD 600 nmstock] on days 4, 6, 8 etc. Tumor volume measurements were made on days15, 19, and 22 and this data appears in FIG. 39 for the four (4) groupsof mice. The data depicted in FIG. 39 sows that there is synergy betweenantigenic composition treatment and an anti-inflammatory (e.g.,Indomethacin) in a subcutaneous cancel model.

On day 11 of the Experiment detailed above, tumors were excised anddigested. Thereafter. The digested tumors were stained with anti-CD11band analyzed by FACS (n=3 per group of mice). The results are depictedin FIG. 40 herein and demonstrate that there is an increased frequencyof CD11b+ cells in the tumors of indomethacin treated mice at day 11post-inoculation.

On day 22 of the Experiment detailed above, tumors were excised anddigested. Thereafter. The digested tumors were stained with anti-CD11band analyzed by FACS (n=7-8 per group of mice). The results are depictedin FIG. 41 herein and demonstrate that there is an increased frequencyof CD11b+ cells in the tumors of indomethacin treated mice at day 22post-inoculation. Further, FIG. 42 demonstrates that indomethacintreatment causes an increase in CD11 b+CD94+ myeloid cells in the tumorsas found at day 22 post-inoculation.

To further examine whether the antigenic composition treatment wasassociated with an anti-inflammatory response, at day 22 of theExperiment described above, whole tumor samples were subjected toquantitative PCR by known methods. The gene products Fizz1 and Ym1 weretargeted. Both Fizz1 and Ym1 are reportedly associated with M2macrophages (see, for e.g., Wong et al. (2010) Eur. J. Immunol. 40(8):2296-307). The results are depicted in FIG. 43 herein. As shown in FIG.43, the relative expression of both Fizz1 and Ym1 was increased intumors where there was treatment of both indomethacin and antigeniccompositions (compared, for example, to indomethacin alone).

The relative expression levels of Arg1 and Fizz1 was examined in boththe tumors and spleens of mice at day 22 of the Experiment. As shown inFIG. 44, both Arg1 and Fizz1 expression increased in the spleens of micetreated with indomethacin and antigenic compositions. The relativeexpression levels of Nos2 and Ym1 was examined in both the tumors andspleens of mice at day 22 of the Experiment. The relative expressionlevels are depicted in FIG. 45 herein for the four (4) groups of mice.

To further examine the anti-inflammatory response associated with theantigenic composition treatment, an experiment was designed as follows.Briefly, mice were given Lewis Lung tumors on day 0 [PBS and K.pneumoniae antigenic composition] or no tumors [PBS (no tumor)] or K.pneumoniae antigenic composition (no tumor)]. The mice received K.pneumoniae antigenic composition [0.1 ml of 0.5 OD500 nm stock] or PBSon day 2, 4, 6, 8. The mice were sacrificed on day 9 and their lungswere removed and homogenized. IFNγ was measured in the lung homogenateusing ELISA. The results are shown in FIG. 46 herein. Treatment with K.pneumoniae antigenic composition reduced IFNγ production in the lungs ofmice with and without lung tumors.

To further examine the anti-inflammatory response associated withantigenic composition treatment, the following experiment was designed.Briefly, bone marrow macrophages were cultured overnight either inmedia, or in medial supplanted with LPS, or in media supplanted with K.pneumoniae antigenic compositions. The media was tested for IL-12 andIL-10. The results are shown in FIG. 47 herein and demonstrate thatIL-12 was not identified. As shown in FIG. 47, bone marrow macrophagescultured overnight with K. pneumoniae antigenic compositions producedIL-10. IL-10 is known to be associated with an anti-inflammatoryresponse (see, for e.g., Bazzoni et al. (2010) Eur. J. Immunol. 40(9):2360-8).

To further examine the anti-inflammatory response associated withantigenic composition treatment, the following experiment was designed.Briefly, the 4T1 tumor model was utilized to determine the effects ofStaph aureus (SA) antigenic composition therapy to work synergisticallywith the anti-inflammatory drug indomethacin. In this study, there werefour (4) groups of 10 Balb/c female mice which all received 50,000 4T1mammary carcinoma cells subcutaneously on day 0. Group 1 received PBSsubcutaneously every 2 days starting on day 4. Group 2 received SA [0.1ml of 0.5 OD 600 nm] subcutaneously every 2 days starting at day 4.Group 3 and 4 received 14 ug/ml of indomethacin (indo) in their drinkingwater and subcutaneously received PBS and SA respectively every 2 daysbeginning on day 4. On day 22 the mice were sacrificed and tumors from7-8 mice per group were harvested and placed in an RNA preserving agent.Subsequently we analyzed the expression of IL-10 in the tumors byreal-time PCR. The results in FIG. 48 show that mice treated withindomethacin and PBS have a significant increase in IL-10 expression inthe tumors. Treatment with indomethacin and SA leads to an even greateramount of IL-10 suggesting that SA enhances the anti-inflammatoryeffects of indomethacin in this tumor model. Since IL-10 is widely knownto be an anti-inflammatory cytokine these results demonstrates that SAworks synergistically with indomethacin in an anti-inflammatory manner.It is important to note that the tumors in the PBS group were thelargest followed by the SA group and the Indo-PBS group. The tumors inthe Indo-SA group were the smallest on day 22.

The anti-inflammatory properties of formulations of the invention can beemployed for use in the treatment of a variety of inflammatory diseases,using endogenous pathogens or exogenous pathogens that are pathogenic inthe tissue or organ within which the inflammation is situated, includingbacterial, viral and fungal pathogens. Table 20 lists diseasescharacterized by inflammation (inflammatory conditions) which may betreated in accordance with alternative aspects of the invention.

TABLE 20 List of Chronic Inflammatory Diseases Acne vulgaris Acutedisseminated encephalomyelitis Acute hemorrhagicleukoencephalitisAddison's Disease Agammaglobulinemia Allergies Alopecia areataAlzheimer's Amyotrophic Lateral Sclerosis Anaemia, autoimmune hemolyticAnaemia, pernicious Ankylosing spondylitis Anti-GBM/TBM NephritisAntiphospholipid syndrome Antisynthetase syndrome Arteritis, temporal(also known as “giant cell arteritis”) Arthritis, juvenile Arthritis,psoriatic Arthritis, reactive (Reiter's syndrome, rea) Arthritis,rheumatoid Asthma Atherosclerosis Atopic allergy Atopic dermatitisAutoimmune enteropathy Autoimmune aplastic anemia Balo disease/Baloconcentric sclerosis Bartter syndrome Bechets Syndrome Berger's diseaseBickerstaff's encephalitis Blau syndrome Bronchitis, chronic Bullouspemphigoid Bursitis Cardiomyopathy, autoimmune Castleman's diseaseCeliac disease Celiac disease Chronic fatigue syndrome Chronicinflammatory demyelinating polyneuropathy Chronic recurrent multifocalosteomyelitis Churg-Strauss syndrome Cicatricialpemphigoid Cirrhosis,primary biliary Cogan syndrome Cold agglutinin disease ColitisComplement component 2 deficiency Connective tissue disease, mixedConnective tissue disease, undifferentiated COPD (chronic obstructivelung disease) Cranial arteritis CREST syndrome CryoglobulinemiaCushing's Syndrome Cutaneous leukocytoclasticangiitis Cystitis,interstitial Dacryadenitis Dego's disease Dercum's disease DermatitisDermatitis herpetiformis Dermatitis, autoimmune progesteroneDermatomyositis Diabetes Diabetes insipidus, nephrogenic Diabetesmellitus type 1 Diffuse cutaneous systemic sclerosis Discoid lupuserythematosus Diverticulitis Dressler's syndrome Dysmenorrhea (menstrualcramps/pain) Eczema Eczema Endometriosis Enthesitis-related arthritisEosinophilic fasciitis Eosinophilic gastroenteritisEpidermolysisbullosaacquisita Erythema nodosum Essential mixedcryoglobulinemia Evan's syndrome FibrodysplasiaossificansprogressivaFibromyalgia Fibrosingaveolitis Gastritis, atrophic Gastritis, atrophicGastrointestinal pemphigoid Giant cell arteritis GlomerulonephritisGlomerulonephritis Goodpasture's syndrome Gout, acute Gout, arthriticGraves' disease Guillain-Barre syndrome (GBS) Haemolytic anaemiaHashimoto's encephalitis Hashimoto's thyroiditis Hemolyticanemia,autoimmune Henoch-Schonleinpurpura Hepatitis, autoimmune Hepatitis,viral Herpes gestationis Hypogammaglobulinemia Idiopathic InflammatoryDemyelinating Diseases Idiopathic pulmonary fibrosis Iga nephropathyIleus (bowel obstruction) Inclusion body myositis Inflammatory boweldisease, Crohn's disease Inflammatory bowel disease, ulcerative colitisInflammatory demyelinating polyneuopathy Inner ear disease, autoimmuneInterstitial cystitis Irritable bowel syndrome (IBS) Juvenile idiopathicarthritis Juvenile rheumatoid arthritis Kawasaki's Disease Kidney stonesLambert-Eaton myasthenic syndrome Leukocytoclasticvasculitis Lichenplanus Lichen sclerosus Linear iga disease (LAD) Lou Gehrig's disease(Also Amyotrophic lateral sclerosis) Lupoid hepatitis Lupus Lupuserythematous Lymphoproliferative syndrome, autoimmune Majeed syndromeMeniere's disease Meningitis Microscopic polyangiitis Miller-Fishersyndrome Morphea Mucha-Habermann disease Multiple sclerosis Multiplesclerosis Myasthenia gravis Myositis Myositis, inclusion body NephritisNephrotic syndrome Neuromyelitisoptica (Also Devic's Disease)Neuromyotonia Occularcicatricialpemphigoid Ocular inflammation (acuteand chronic non-bacterial inflammation of the anterior part of the eyes)Opsoclonus myoclonus syndrome Ord thyroiditis Osteoarthritis Paget'sdisease of bone Palindromic rheumatism Pancreatitis, autoimmune PANDAS(pediatric autoimmune neuropsychiatric disorders associated withstreptococcus) Paraneoplastic cerebellar degeneration Parkinson'sParoxysmal nocturnal hemoglobinuria (PNH) Parry Romberg syndrome Parsplanitis Parsonnage-Turner syndrome Pelvic inflammatory diseasePemphigus Pemphigus vulgaris Pericarditis, non-rheumatic Peripheralneuropathy, autoimmune Perivenous encephalomyelitis POEMS syndromePolyarteritisnodosa Polychondritis, relapsing Polyendocrine syndrome,autoimmune Polymyalgia rheumatica Polymyalgia rheumatica PolymyositisPrimary sclerosing cholangitis Progressive inflammatory neuropathyProstatitis, chronic Pseudogout Psoriasis Psoriasis Pure red cellaplasia Pyodermagangrenosum Rasmussen's encephalitis Raynaud phenomenonReiter's syndrome Restless leg syndrome Retinopathy of prematurityRetroperitoneal fibrosis Rheumatoid fever Rhinitis, allergic SarcoidosisSarcoidosis Schmidt syndrome Schnitzler syndrome Scleritis SclerodermaSclerosis, systemic Sjogren's syndrome Spondyloarthropathy Still'sdisease Subacute bacterial endocarditis (SBE) Susac's syndrome Sweet'ssyndrome Sydenham chorea Sympathetic ophthalmia Takayasu's arteritisTemporomandibular joint disorder (TMJD or TMD), or TMJ syndromeThrombocytopenic purpura, autoimmune Thrombocytopenic purpura,idiopathic Tolosa-Hunt syndrome Transplant rejection Transverse myelitisUndifferentiated spondyloarthropathy Urticaria Uveitis, autoimmuneValvular disease, non-rheumatic Vasculitis Vitiligo Wegener'sgranulomatosis

As provided in Table 20 above, arthritis is a chronic inflammatorydisease. In particular, arthritis is understood to be a description ofinflammation of one or more joints. There are many types of arthritis,which include (but are not limited to) the following: Ankylosingspondylitis, Behcet's disease, Ehlers-Danlos Syndrome, FamilialMediterranean fever, Fibromyalgia, Fifth disease, Giant cell arteritis,Gout, Haemochromatosis, Henoch-Schönleinpurpura, HyperimmunoglobulinemiaD with recurrent fever, Inflammatory bowel disease arthritis (includingCrohn's Disease and Ulcerative Colitis), Juvenile rheumatoid arthritis,Juvenile spondyloarthropathy, Lyme disease, Marfan syndrome,Osteoarthritis, Pseudo-gout, Psoriatic arthritis, Reactive Arthritis(Reiter's syndrome), Rheumatoid arthritis, Sarcoidosis, Scleroderma, SEAsyndrome (seronegativity, enthesopathy, arthropathy), Sjogren'ssyndrome, Still's disease, Systemic lupus erythematosus (SLE), TNFreceptor associated periodic syndrome, and Wegener's granulomatosis (andother vasculitis syndromes).

In alternative aspects of the invention, arthritis can be treated usingformulations of the invention that include pathogens, such as bacteria,that infect joint regions. For example, the following bacteria/bacterialspecies, known to infect the joint regions, may be used in formulationsof the invention for treating an arthritis: Staphyloccus aureus;Coagulase negative Staphylococci; Streptococcus pneumoniae;Streptococcus species; Pseudomonas aeruginosa; Mycobacteriumtuberculosis; Neisseria meningitides; Mycobaterium bovis; Enterococcusspecies; Salmonella enteritidis; Escherichia coli; Proteus species;Serratia species; Acinetobacter species; Enterobacter species;Pasteurella species; Campylobacter species; Brucella species;Haemophilus influenza; Neisseria gonorrhoeae; Mycobacterium xenopi;Mycobacterium leprae; Coxiella bumetti; Bartonella species; ActinomaduraMadura; Streptomyces somaliensis; Borrelia burgdorferi; and Yersiniaspecies. Further, and for example, the following viral species are knownto infect the joint regions: Enterovirus; Dengue virus; Hepatitis B;Hepatitis C; HIV; Human parovirus; Mumps virus and Rubella. Further, thefollowing fungal species are known to infect the joint regions:Coccidioides immitis; Candida albicans; Blastomyces dermatitidis;Histoplasma capsulatum; Cryptococcus neoformans; Paracoccidioidesbrasiliensis; Sporothrix schenckii; and Penicillium mameffi. Further,and for example, the following helminth or protozoa species are known toinfect the joint regions: Loa loa; Mansonella streptocerca; Onchocercavolvulus; Dracunculus medinersis; Gnathostoma spinigerum; Schistomsomaspecies; Strongyloides stercoralis; Echinococcus species; Trichinellaspiralis; and Giardia species. The foregoing examples arerepresentative, and are not limiting.

In alternative aspects, arthritis may be treated using preparations madewith one or more endogenous pathogens: Staphyloccus aureus; Coagulasenegative Staphylococci; Streptococcus pneumoniae; Streptococcus species;Pseudomonas aeruginosa; Enterococcus species; Salmonella enteritidis;Escherichia coli; Proteus species; Serratia species; Acinetobacterspecies; Enterobacter species; Pasteurella species; Campylobacterspecies; or Haemophilus influenza. Alternatively, the pathogen may beexogenous: Mycobacterium tuberculosis; Neisseria meningitides;Mycobaterium bovis; Brucella species; Neisseria gonorrhoeae;Mycobacterium xenopi; Mycobacterium leprae; Coxiella burnetti;Bartonella species; Actinomadura Madura; Streptomyces somaliensis;Borrelia burgdorferi; and Yersinia species. Alternatively, the pathogenmay be a virus: Enterovirus; Dengue virus; Hepatitis B; Hepatitis C;HIV; Human parovirus; Mumps virus and Rubella. Alternatively, thepathogen may be a fungal species: occidioides immitis; Candida albicans;Blastomyces dermatitidisl; Histoplasma capsulatum; Cryptococcusneoformans; Paracoccidioides brasiliensis; Sporothrix schenckii; andPenicillium mameffi. Alternatively, the pathogen may be a helminth orprotozoa species: Loa loa; Mansonella streptocerca; Onchocerca volvulus;Dracunculus medinersis; Gnathostoma spinigerum; Schistomsoma species;Strongyloides stercoralis; Echinococcus species; Trichinella spiralis;and Giardia species.

In further alternative embodiments, arthritis may be treated usingpreparations made with bacterial pathogens that are common causes ofbone infection: Staphylococcus aureus, coagulase-negative staphylococci,Streptococcus pyogenes, Streptococcus pneumoniae, Streptococcusagalactiae, other streptococci spp., Escherichia coli, Pseudomonas spp.,Enterobacter spp., Proteus spp., Serratia spp., Neisseria gonorrhea,Salmonella spp., Mycobacterium tuberculosis, Haemophilus influenza; or,common viral pathogens parvovirus B19, rubella, hepatitis B; or, acommon fungal pathogen: Scedosporium prolificans.

Example 12: Inflammatory Bowel Disease Studies

This example provides an illustration of the clinically effective use ofan antigenic formulation comprising killed E. coli in the treatment of apatient with Crohn's disease, over a three-month course of treatment.During the course of treatment, the patient became symptom free andceased using anti-inflammatory medications.

The patient initially presented reporting pain in the area of the largeintestine and diarrhea, while under treatment with prednisone andImuran™.

Treatment was initiated with a subcutaneous inoculum of a killedformulation of whole E. coli, derived from an E. coli strain collectedfrom a patient with an E. coli colonic infection. The dosing scheduleinvolved a subcutaneous dose every second day, beginning with a 0.05 mldose, gradually increasing in volume until a 2 inch diameter lightpink/red skin response was achieved within 24 hours after injection atthe injection site. The dose eventually required to achieve this skinresponse was 0.09-0.11 ml in this patient, and this dose has beencontinued as a maintenance dose every second day.

One week following the initiation of treatment with the antigenicpreparation of whole killed E. coli, the patient reported that the painand diarrhea were gone. Within about two months, the patientdiscontinued treatment with prednisone while continuing on a daily doesof 150 mg of Imuran™. Subsequently, the patient also discontinued use ofImuran™.

By two-months following the initiation of treatment with the E. colicomposition, the patient was self-administering 0.09-0.11 ml of the E.coli preparation every other day. The patient self-adjusted this dosageso as to provoke a local inflammatory reaction evidenced by a pink spotof approximately 2 inches in diameter that persisted at the site ofadministration for about two days. This patient is also described inlater studies detailed in Example 15 herein.

Example 13: Fungal Studies

Experiments utilizing the lung mouse model system described in detailherein were conducted which determined that mice that had received watercontaminated with a particular fungal species (Penicillium marneffei),which is known to cause respiratory infections in both mice and humans,demonstrated decreased tumor burden as has been demonstrated anddiscussed with respect to bacterial lung pathogens.

Numerous fungal species are known to be associated with various organsor tissues as detailed in Table 21 below that water contaminated withfungal species also resulted. Accordingly, and based on the experimentalprinciples detailed herein, the specificity demonstrated herein withrespect to bacterial and viral pathogens should be extendable to fungalpathogens as well.

TABLE 21 Fungal species and associations with organs/tissues Duo-denumFungus Skin Respiratory Genital GU system Mouth Stomach Jejunum IleumColon Other Actinomadura X species Alternaria species X sinusesAspergillus X sinuses, fumigatus brain Bipolaris species X sinusesBlastomyces X X X bones species Candida alibcans X X X X œesophagusCandida krusei Cladophialophora X sinuses carrionii Coccidiodes immitisX Coccidiodes posadasii Cryptococcus X neoformans Cryptococcus gattiiCurvularia species X sinuses Epidermophyton X species Exophiala speciesX sinuses Fonsecaea pedrosoi X Fusarium species X X sinuses HistoplasmaX capsulatum Microsporum X species Nocardia species X Paecilomyces X Xsinuses species Paracoccidioides X X X brasiliensis Pityrosporum Xspecies Penicillium marneffei X X systemic infection Pneumocystis Xjiroveci Pseudallescheria X X sinuses boydii (Scedosporium apiospermum)Rhizopus species X X X X X sinuses, (Rhizo)Mucor orbits, brain, speciesAbsidia species Cunninghamella species Scedosporium X X sinusesprolificans Sporothrix schenckii X Stachybotrys X chartarum Tineacapitis X Tinea cruris Tinea pedis Trichoderma X X sinuseslongibrachiatium Trichophyton X species Trichosporon X X sinuses species

Example 14: Arthritis Studies

Patient BA. Patient BA was diagnosed at age 18 with Crohn's disease. Inaddition to gastrointestinal symptoms associated with Crohn's disease,she also had Crohn's arthritis symptoms (join aches and stiffness), themost common extraintestinal manifestation of Crohn's disease. She wastreated with prednisone, Remicade™ and other medications, but continuedto have symptoms in spite of this treatment. At the age of 33, thepatient was continuing to have ongoing symptoms of abdominal pain anddiarrhea and joint pain and stiffness in spite of treatment withlong-term prednisone. Her joint symptoms were severe. She described herjoint symptoms and their impact on her life as feeling like a “frozensnowman” due to the joint pain and stiffness. On Aug. 22, 2011, thepatient started treatment with antigenic compositions derived from E.co/i. More specifically, treatment was initiated with a subcutaneousinoculum of a killed formulation of whole E. coli, derived from an E.coli strain collected from a patient with an E. coli colonic infection.Within 4 days of starting the E. coli treatment described herein, hergastrointestinal symptoms resolved completely and remained in remissionwith E. coli treatment.

However, her joint symptoms (not targeted by E. coli antigeniccompositions) continued unabated. She was still having severe joint pain(shoulders, hands, neck, low back, knee) and joint stiffness in spite oftreatment with 20 mg prednisone daily and ibuprofen. On Sep. 25, 2011,Patient BA began treatment with antigenic compositions derived from S.aureus, given every second day by s.c. injection, to target herarthritis symptoms (S. aureus is the most common cause of bone and jointinfection). More specifically, treatment was initiated with asubcutaneous inoculum of a killed formation of whole S. aureus, derivedfrom a S. aureus strain collected from a patient with a S. aureusabscess infection. She began treatment with a dose of 0.05 ml andgradually increased the dose until a 1-2 inch (diameter) light pink/redskin response was achieved 24 hours after the injection at a dose of0.25 ml, which she then maintained every second day. After 10 days oftreatment with antigenic compositions derived from S. aureus, her jointsymptoms began to improve with decreased joint pain and symptoms and thepatient began weaning off prednisone. Her joint symptoms continued toimprove and she discontinued prednisone and no longer required ibuprofenfor pain. After 2 months of treatment with S. aureus as describedherein, this patient's joint symptoms had resolved completely. Threemonths after starting S. aureus treatment as described herein, thepatient remains free of joint symptoms and fully active.

Patient BB.

Patient BB had severe rheumatoid arthritis with severe bone deformity,joint pain and morning stiffness which was resistant to treatment withPlaquenil™, methotrexate, prednisone and other standard treatments.Rheumatoid factor 343 IU/ml (normal 0-20 IU/ml). At the time Patient BBbegan treatment with S. aureus, she was on treatment with long-termmethotrexate, 20 mg prednisone and a non-steroidal anti-inflammatoryagent (NSAID). Patient BB started on treatment with antigeniccompositions derived from S. aureuson Nov. 14, 2011 by s.c. injectionevery second day. She gradually increased the dose of antigeniccompositions derived from S. aureus from 0.05 ml to 0.10 ml until a 1inch diameter skin response was achieved at the injection site 24 hoursafter s.c. injection. She has maintained this dose every second day,with a 1 inch skin response at the site of injection 24 hours afterinjection. By Dec. 6, 2011, 3 weeks after the treatment had begun asdescribed herein, her symptoms had begun to improve significantly. ByDec. 20, 2011, after 5 weeks of treatment as described herein, PatientBB reported that joint symptoms had improved further and that hermorning stiffness had “reduced tremendously”. She discontinuedmethotrexate treatment. She continued to improve and, by Jan. 6, 2011,after 7 weeks of treatment with antigenic compositions derived from S.aureus, her morning stiffness had resolved completely and her joint painthroughout the rest of the day had improved significantly (from a scoreof 6/10 to 3/10). This positive result with antigenic compositionsderived from S. aureus treatment was particularly surprising to thepatient since her disease symptoms had been previously resistant toother arthritis treatments.

Example 15: Crohn's Disease Studies

Patient AA.

This patient was previously described at an earlier time point inExample 12. This example provides a further and continued illustrationof the clinically effective use of an antigenic formulation comprisingkilled E. coli in the treatment of a patient with Crohn's disease, overan eleven-month course of treatment with complete sustained remission ofdisease. During the course of treatment, the patient became symptom freeand ceased using anti-inflammatory medications. The patient wasdiagnosed with Crohn's disease in July 2006, with symptoms of bloodydiarrhea and weight loss (30 pound weight loss). Colonoscopy revealedCrohn's disease in the cecum, ascending, transverse and descendingcolon. He began on treatment with Imuran™ and intermittent treatmentwith prednisone. In spite of these medications, his symptoms ofabdominal pain and loosed stools persisted with flare ups of bloodydiarrhea. In July 2010, his symptoms worsened in spite of treatment withImuran and prednisone. He began treatment with antigenic compositionsderived from E. coli on Jul. 26, 2010. Treatment was initiated with asubcutaneous inoculum of a killed formulation of whole E. coli, derivedfrom an E. coli strain collected from a patient with an E. coli colonicinfection. The dosing schedule involved a subcutaneous dose every secondday, beginning with a 0.05 ml dose, gradually increasing in volume untila 2 inch diameter light pink/red skin response was achieved within 24hours after injection at the injection site. The dose eventuallyrequired to achieve this skin response was 0.09-0.11 ml in this patient,and this dose was continued as a maintenance dose every second day. Thepatient self-adjusted the dosage so as to provoke a local inflammatoryreaction evidenced by a pink spot of approximately 2 inches in diameterthat persisted at the site of administration for about two days.

After 1 week of treatment with antigenic compositions derived from E.coli, the patient's symptoms of abdominal pain and diarrhea resolvedcompletely and he was able to return to work. He began weaning off ofprednisone and discontinued prednisone on September 15^(th). After 3weeks of treatment as described herein, he had gained 14 pounds and wasfeeling in excellent health. On Sep. 28, 2010, a repeat colonoscopyshowed no signs of Crohn's disease activity. On Oct. 18, 2010, thepatient stopped Imuran treatment.

The patient remained completely symptom free and in excellent health,the first time he had felt well since his diagnosis of Crohn's disease 4years before. While stress, travel, or alcohol had precipitated flareups previously, the patient was now able to travel and eat or drinkwhatever he liked and he remained symptom free. He regained 26 poundsand was able to return to a full and active life.

On Jul. 1, 2011, after eleven months of treatment with antigeniccompositions derived from E. coli, the patient remained symptom free andin excellent health and discontinued treatment on that date. Six monthslater, in January, 2012, the patient remains symptom free and in fullsustained clinical remission from Crohn's disease.

Patient AB.

Patient AB was diagnosed with Crohn's disease in November 2009 bycolonscopy, after having abdominal pains since July 2009. The patientinitially declined treatment. However, her symptoms worsenedsubstantially, with severe abdominal pain, bloody stool and 15 poundweight loss. She was hospitalized June 25^(th), 2011, at which time shewas treated with i.v. fluids and antibiotics. She took two doses ofprednisone but then discontinued prednisone treatment due to concernswith respect to potential side effects. On Jul. 27, 2010, she begantreatment with antigenic compositions derived from E. coli by s.c.injection every second day, beginning with a dose of 0.05 ml andgradually increasing the dose till a 2 inch diameter light pink skinresponse was achieved at the site of injection 24 hours after injectionat a dose of 0.10 ml. The 0.10 ml was then continued as the maintenancedose, with the resultant 2 inch skin response following each s.c.injection. During the period prior to the initiation of the treatmentwith antigenic compositions derived from E. coli, the patient was havingcramping abdominal pain with bloating and loose stools. Within 3 days ofstarting the treatment as described herein, the patient'sgastrointestinal symptoms resolved completely and the patient's bowelmovements became well-formed and regular, the first time that she hadregular bowel movements “in years”. Patient AB's symptoms remained incomplete remission and she continued treatment with antigeniccompositions derived from E. coli for 3 months. After 3 months oftreatment, she discontinued treatment. Two months after stopping thetreatment as described herein, the patient remains symptom free and infull clinical remission from Crohn's disease.

Patient AC.

Patient AC was diagnosed with Crohn's disease in July 2007 bycolonoscopy. She was treated with Asacol™, but was having crampingabdominal pains and 3-4 bowel movements per day in spite of thistreatment. She would get “flare ups” with constant abdominal pain if sheate certain foods (e.g., high fibre foods, dairy). On Jul. 7, 2011,Patient AC began treatment with antigenic compositions derived from E.coli by s.c. injection every second day, with an initial dose of 0.05 mlgradually increasing till a 1-2 inch diameter pink skin response wasachieved at the injection site 24 hours after injection at a dose of 0.1ml, which she then maintained every second day. Within one week ofstarting the treatment as described herein, her gastrointestinalsymptoms resolved completely and she began having normal once-dailybowel movements. She began eating foods that previously would havecaused ‘flare ups’ and did not have any symptoms after consuming thesefoods. After 5 weeks of the treatment with antigenic compositionsderived from E. coli, Patient AC discontinued Asacol treatment. Eventhough in the past when she missed an Asacol dose she would get aflare-up, she remained symptom free after stopping Asacol while ontreatment with antigenic compositions derived from E. coli. After 3.5months of treatment as described herein, Patient AC remained in completeclinical remission from Crohn's disease and discontinued SSI treatmenton Oct. 25, 2011. Two months after stopping treatment with antigeniccompositions derived from E. coli, the patient remains symptom free andin full clinical remission from Crohn's disease.

Patient AD.

Patient AD was diagnosed with Crohn's disease in 1998 by colonoscopy.She was treated with various Crohn's disease treatments in the past,including prednisone, Purinethol™, Pentasa™, and Entocort EC™ withoutimprovement of disease symptoms and therefore, she discontinued thesetreatments. Patient AD began treatment with antigenic compositionsderived from E. coli on 29 Aug. 2011, at which time she was havingcramping abdominal pains with diarrhea (3-5 loose bowel movements perday). Patient AD's Crohn's symptoms began to improve 2 weeks afterinitiation of the treatment. After 2.5 months of treatment, Patient ADwas symptom free, with one normal firm bowel movement per day, the firsttime she had had normal regular bowel movements since her diagnosis withCrohn's disease 13 years previously. 4 months after starting thetreatment with antigenic compositions derived from E. coli, Patient ADremains on treatment with antigenic compositions derived from E. coliand in full clinical remission from Crohn's disease.

Patient AE.

Patient AE was diagnosed at age 18 with Crohn's disease. She was treatedwith prednisone, Remicade™ and other medications, but continued to havesymptoms in spite of these treatments, and therefore, had discontinuedall other treatments except prednisone. At the age of 33, the patientwas continuing to have ongoing symptoms of abdominal pain and diarrheain spite of treatment with long-term prednisone. On Aug. 22, 2011, thepatient started treatment with antigenic compositions derived from E.coli, with an initial dose of 0.05 ml s.c., gradually increased till a1-2 inch pink skin response occurred 24 hours after injection, at a doseof 0.08 ml, which the patient then maintained every second day. Within 4days of starting the treatment as described herein, the patientsgastrointestinal symptoms resolved completely, which the patientdescribed as “very surprising and fantastic” considering that she hadbeen on many other Crohn's medications in the past without resolution ofher symptoms. The patient weaned off prednisone treatment and remainedsymptom free on treatment with antigenic compositions derived from E.co/i. Four months after starting the treatment, the patient remains freeof Crohn's gastrointestinal symptoms and in full clinical remission onthe treatment.

Patient AF was diagnosed with severe Crohn's disease in 1995, withdisease throughout his small and large intestine. He had been treatedwith many different Crohn's disease medications, including Remincade™,Asacol™, prednisone and many other treatments and experimentaltherapies, without success in controlling his disease. He had hadmultiple surgeries and hospitalizations. Prior to the initiation oftreatment with antigenic compositions derived from E. coli, he had beenon daily prednisone (20 mg per day) for 7 years. Patient AF begantreatment with antigenic compositions derived from E. coli on Sep. 16,2011. At that time, he was having constant cramping abdominal pain with20 loose/watery bowel movements per day. He began with a dose (ofantigenic compositions of E. coli) of 0.05 ml and gradually increasedthe dose until a 1 inch diameter skin response was achieved 24 hoursafter s.c. injection at a dose of 0.15 ml, which he has continued as as.c. maintenance dose every second day. Within 1 week of startingtreatment with antigenic compositions derived from E. coli, his symptomsof abdominal cramping resolved. After 1 month of the treatment, hisbowel movements became firmer and bowel movement frequency has reducedfrom 20 bowel movements per day to 5-10 bowel movements per day. After 4weeks of the treatment as described herein, Patient AF began reducingthe dose of prednisone. In the past, reducing the dose of prednisoneresulted in worsening of Crohn's symptoms. While on treatment withantigenic compositions derived from E. coli, reducing prednisone dosedid not result in worsening of symptoms. After 3.5 months of thetreatment, patient AF has reduced his dose of prednisone to 5 mg per day(from 20 mg per day prior to the start of the treatment), has remainedfree of abdominal pain for 3 months and has substantially less bowelmovements per day (5-10 vs. 20) than when he began treatment withantigenic compositions derived from E. co/i, indicating that, while notin remission, his Crohn's disease and clinical symptoms havesubstantially improved on the treatment with antigenic compositionsderived from E. coli.

Example 16: Mouse Colitis Studies Disease Studies

A DSS-induced colitis model was developed (see, for e.g., Pizarro et al.(2003) TRENDS in Molecular Medicine 9(5)). Briefly, groups of 5 femaleC57BL/6 mice were given 3% DSS in their drinking water from Day 0-7.Either antigenic compositions derived from E. coli or PBS wereadministered 0.05 ml subcutaneously every 2 days starting on day 0. Theweight of the animals was monitored daily for 7 days and data in FIG. 49herein represents the average weight change of the mice over the courseof treatment. Mice treated with antigenic compositions derived from E.coli lost less weight.

On day 7 of the experiment, the mice were sacrificed and their colonswere removed and homogenized. As shown in FIG. 50 herein, IL-17 levelsin E. coli treated mice are reduced compared to PBS treated control micein the colon 7 days after the start of DSS treatment. IL-17AF levelswere measured in the homogenized colon samples using a bead array.

Further, in a related study the efficacy of treating dextran sulphatesodium(DSS)-induced murine colitis with antigenic compositions derivedfrom E. coli was illustrated. Colitis was induced in BALB/c mice by 3.5%DSS dissolved in the drinking water for 10 days. Placebo or antigeniccompositions derived from E. coli (0.03 mL of undiluted SSI) wasadministered subcutaneously every other day beginning on the first dayof 3.5% DSS exposure. To assess in vivo efficacy, a clinical diseaseactivity score was evaluated daily. Specifically, the body weight,occult blood or the presence of gross blood per rectum, and stoolconsistency were determined daily as described previously (Dieleman etal., 1997; Hartmann et al., 2000; Siegmund et al., 2001). The score wasderived as follows: weight loss <1% counted as 0 points, weight loss of1 to <5% as 1 point, 5 to <10% as 2 points, 10 to 20% as 3 points, andmore than 20% as 4 points. For stool consistency, 0 points were givenfor well formed pellets; 2 points for pasty and semi-formed stools,which did not stick to the anus, and 4 points for liquid stools that didstick to the anus. Bleeding was scored 0 points for no blood inhemoccult; 2 points for positive hemoccult; and 4 points for grossbleeding. The average of these three scores (body weight, stoolconsistency, and rectal bleed) gave an overall clinical score. The datais represented in FIG. 51 herein. The results of this study demonstratea trend towards a decrease in colitis disease clinical score when micereceived antigenic compositions derived from E. coli with day 10reaching significance (p-value=0.0442 using unpaired, two-tailedT-test), relative to PBS.

Further, in a related study, the effect of treatment with antigeniccompositions derived from E. coli was investigated to determine itsefficacy in dextran sulphate sodium (DSS)-induced murine colitis.Colitis was induced in 10 C57BL/6 mice by giving 3% DSS dissolved in thedrinking water for 7 days prior to placebo or E. coli antigeniccomposition treatment. Water containing DSS was replaced with regulardrinking water and placebo or antigenic compositions derived from E.coli (0.05 mL of undiluted SSI) was administered subcutaneously everyother day beginning on day 7 post 3% DSS exposure. To assess in vivoefficacy, protection from weight loss due to DSS-induced colitis, thebody weight was measured daily. There were 5 mice per treatment group.The average percent weights of the mice in their respective groups wereplotted.

The results of this study demonstrate a decrease in colitis disease asmeasured by protection from weight loss when mice, which had colitisinduced with DSS from days 1 to 6, received treatment with antigeniccompositions derived from E. coli from days 7 to 15, which reachedstatistical significance (p-value <0.04 using unpaired, two-tailedT-test), relative to PBS. Treatment of mice with antigenic compositionsderived from E. coli has a therapeutic benefit after colitis wasinduced. The results are depicted in FIG. 52.

Example 17: Personalized Site-Specific Immunomodulation Studies

The clinical and preclinical data on the site-specificity of killedbacterial preparations for the treatment of cancer and chronicinflammation provide support for the view that the host immune system isable to recognize the bacteria and mount an immune response where thatbacterium is likely to cause an infection. Accordingly, we testedwhether a previous exposure to a bacterial species determines whether anantigenic composition comprised of components of that bacterial speciescan induce a site-specific immune response.

In order to test this hypothesis, a study was conducted where we havemeasured the therapeutic efficacy of S. pneumoniae antigeniccompositions for the treatment of lung cancer in mice that have eithernever been exposed to S. pneumoniae (note: not a natural lung pathogenin mice), are currently colonized by S. pneumoniae, or were previouslyexposed to S. pneumoniae but have cleared the colonization before thestart of the study (see: Experimental Setup in Table 22).

TABLE 22 Experimental Setup for Personalized Site-SpecificImmunomodulation Studies Day −21 Day −3 Day 0 1 2 3 4 5 6 7 8 9 10 21 IsSSI treatment more/less/equally effective in mice that have previouslybeen or are currently colonized with S. pneumoniae? Group 1A ColonizeLLC SSI SSI SSI SSI SSI Terminate experiment with strain P1121 Group 1Bsaline LLC SSI SSI SSI SSI SSI Terminate experiment (no mice expected tosurvive in this group) Group 1C LLC Terminate experiment Group 1DColonize LLC SSI SSI SSI SSI SSI Terminate experiment with strain P11211st collection 2nd collection In the first and second collections 5 miceper group will be sacrificed and lung flow (MDSC, T cells, NK myeloidcells assessed), cytokines (lung & serum), histology performed, tumournodules counted etc At least 10 mice will be in each group for survivalstudies.

For these studies, mice were challenged intranasally with a strain of S.pneumoniae (P1121) which normally colonizes the nasal cavity of humansand which can cause acute colonization in mice (see, for e.g. McCool andWeiser (2004), Limited role of antibody in clearance of Streptococcuspneumoniae in a murine model of colonization. Infect Immun., 72(10): p.5807-13; and van Rossum et al. (2005) Host and bacterial factorscontributing to the clearance of colonization by Streptococcuspneumoniae in a murine model. Infect Immun., 73(11): p. 7718-26). Twogroups of mice received no S. pneumoniae challenge, 1 group received S.pneumoniae on Day −28 (past exposure), and the last group received S.pneumoniae on Day −3 (current exposure) (see: Table 22). On Day 0 allmice received Lewis Lung Carcinoma (LLC) cells intravenously. Startingon Day 2, three of the four groups started receiving subcutaneoustreatment with S. pneumoniae antigenic composition which was continuedevery two days until death. Mice which had never been exposed to S.pneumoniae showed no survival benefit when treated with S. pneumoniaeantigenic composition. This was expected based on the fact that S.pneumoniae is not a natural lung pathogen in mice. Strikingly however,lung cancer-bearing mice that were either currently colonized or hadpreviously cleared pulmonary S. pneumoniae colonization survivedsignificantly longer when treated with S. pneumoniae antigeniccomposition (see FIG. 53). These results indicate that previous exposureto a particular bacterial species is a predetermining factor of theefficacy of an antigenic composition generated from that bacterialspecies. Accordingly, personalized site-specific immunomodulation can bedeveloped for a subject based on a subject's prior exposure to aparticular pathogen species, such as a bacterial pathogen as detailedherein. Personalized site-specific modulation based on prior exposure toa pathogen is not limit to bacterial pathogens; rather, as detailedherein, it is specifically contemplated that prior exposure to viralpathogens, fungal pathogens, protozoan pathogens, and helminth pathogenswould elicit the same immunological response.

Accordingly, In one aspect, a method of treating an individual for acondition characterized by inflammation in a specific organ or tissue.The method involves determining whether the individual has previouslybeen infected with at least one pathogen that is pathogenic in thespecific organ or tissue; and administering to the individual ananti-inflammatory composition comprising antigenic determinants, theantigenic determinants selected or formulated so that together they arespecific for the at least one pathogen.

In another aspect, a method of formulating an anti-inflammatorycomposition for treating an individual for a condition characterized byinflammation in a specific organ or tissue. The method involvesdetermining whether the individual has previously been infected with atleast one pathogen that is pathogenic in the specific organ or tissue;producing an antigenic composition comprising antigenic determinantsthat together are specific for the at least one pathogen; andformulating the antigenic composition for administration as ananti-inflammatory composition capable of eliciting an anti-inflammatoryresponse in the specific organ or tissue.

The methods detailed herein may involve identifying the presence of atleast one antibody that recognizes the at least one pathogen. Themethods may involve identifying at least one memory B cell thatrecognizes the at least one pathogen. The methods may involveidentifying at least one memory T cell that recognizes the at least onepathogen. The methods may involve the at least one antibody, the atleast one memory B cell, or the at least one memory T cell beingobtained from peripheral circulation of the individual.

In another aspect, a method of treating an individual for a conditioncharacterized by inflammation in a specific organ or tissue. The methodinvolves administering to the individual an infectious dose of at leastone pathogen that is pathogenic in the specific organ or tissue; andadministering to the individual an anti-inflammatory compositioncomprising antigenic determinants, the antigenic determinants selectedor formulated so that together they are specific for the at least onepathogen. The method may involve these two administration stepsoccurring simultaneously. The method may involve the second stepoccurring between 1 hour and 30 days after the first step.

As used herein the term “infectious dose” means a dose that issufficient to result in infection in a specific organ or tissue withoutresulting in systemic infection in the individual.

The methods detailed herein may involve a tumour being situated in thespecific organ or tissue of the individual.

The methods detailed herein may involve the anti-inflammatorycomposition being formulated for subcutaneous injection or intradermalinjection. Further, the anti-inflammatory composition may be formulatedfor repeated subcutaneous or intradermal injection. Further, theanti-inflammatory composition may be formulated for injection to producea localized skin immune response at a site of administration.

Further, the methods detailed herein may involve the at least onepathogen being endogenous to the specific organ or tissue. Further, themethods detailed herein may involve the at least one pathogen beingexogenous to the specific organ or tissue. Further, the methods detailedherein may involve killing the at least one pathogen to formulate theantigenic composition as a whole killed pathogen composition. Further,and without limitation, the at least one pathogen may be a bacterium, avirus, a protozoa, a fungus, or a helminth.

OTHER EMBODIMENTS

Although various embodiments of the invention are disclosed herein, manyadaptations and modifications may be made within the scope of theinvention in accordance with the common general knowledge of thoseskilled in this art. Such modifications include the substitution ofknown equivalents for any aspect of the invention in order to achievethe same result in substantially the same way. Numeric ranges areinclusive of the numbers defining the range. In the specification, theword “comprising” is used as an open-ended term, substantiallyequivalent to the phrase “including, but not limited to”, and the word“comprises” has a corresponding meaning. Citation of references hereinshall not be construed as an admission that such references are priorart to the present invention. All publications are incorporated hereinby reference as if each individual publication were specifically andindividually indicated to be incorporated by reference herein and asthough fully set forth herein. The invention includes all embodimentsand variations substantially as hereinbefore described and withreference to the examples and drawings.

1-20. (canceled)
 21. A method for treating a patient having ulcerativecolitis, the method comprising: administering to a patient, diagnosed ashaving ulcerative colitis and exhibiting symptoms of ulcerative colitis,intradermally or subcutaneously an amount of an antigenic formulationcomprising whole killed Escherichia coli (E. coli) cells in successivedoses given at a dosage interval of at least one hour so that two ormore doses are administered over a period from four days to one week,over a dosage duration of at least one week, wherein the amount of theantigenic formulation and duration of the administering istherapeutically effective to reduce or eliminate the symptoms ofulcerative colitis in the patient, wherein the whole killed E. colicells are cells of an E. coli strain that is pathogenic in a humancolon.
 22. The method of claim 21, wherein the patient is a humanpatient.
 23. The method of claim 22, wherein the dosage duration is atleast two weeks.
 24. The method of claim 23, wherein the antigenicformulation is administered so that each dose is effective to cause avisible localized inflammatory immune response at an administrationsite.
 25. The method of claim 24, wherein the antigenic formulation isadministered so that the visible localized inflammation at theadministration site occurs within one to 48 hours.
 26. The method ofclaim 25, wherein the whole killed E. coli cells are cells of an E. colistrain collected from a human patient with an E. coli colonic infection.27. The method of claim 25, wherein the antigenic formulation isadministered subcutaneously every day, or every other day.
 28. Themethod of claim 22, wherein the whole killed E. coli cells are cells ofan E. coli strain collected from a human patient with an E. coli colonicinfection.
 29. The method of claim 28, wherein the dosage duration is atleast two weeks.
 30. The method of claim 29, wherein the antigenicformulation is administered so that each dose is effective to cause avisible localized inflammatory immune response at an administrationsite.
 31. The method of claim 26, wherein the antigenic formulation isadministered subcutaneously every day, or every other day.
 32. Themethod of claim 28, wherein the antigenic formulation is administered sothat each dose is effective to cause a visible localized inflammatoryimmune response at an administration site.
 33. The method of claim 32,wherein the antigenic formulation is administered so that the visiblelocalized inflammation at the administration site occurs within one to48 hours.
 34. The method of claim 28, wherein the antigenic formulationis administered subcutaneously every day, or every other day.
 35. Themethod of claim 22, wherein the antigenic formulation is administered sothat each dose is effective to cause a visible localized inflammatoryimmune response at an administration site.
 36. The method of claim 35,wherein the antigenic formulation is administered so that the visiblelocalized inflammation at the administration site occurs within one to48 hours.
 37. The method of claim 36, wherein the antigenic formulationis administered subcutaneously every day, or every other day.
 38. Amethod for treating a human patient having ulcerative colitis, themethod comprising: administering to a human patient, diagnosed as havingulcerative colitis and exhibiting symptoms of ulcerative colitis, anamount of an antigenic formulation comprising whole killed Escherichiacoli (E. coli) cells of an E. coli strain collected from a patient withan E. coli colonic infection, in successive doses subcutaneously at adosage interval of every day or every other day, so that two or moredoses are administered over a period from four days to one week, over adosage duration of at least two weeks, wherein the dose of antigenicformulation is effective to cause a visible localized inflammatoryimmune response at an administration site within one to 48 hours,wherein the amount of the antigenic formulation and duration of theadministering is therapeutically effective to reduce or eliminate thesymptoms of ulcerative colitis in the patient, and wherein the E. colistrain is pathogenic in a human colon.